@Override
 public void setup(final Collection<? extends Atom> atoms) {
   for (final Atom atom : atoms) {
     if (atom.getType() != BasicType.B && atom.getType() != BasicType.C) {
       continue;
     }
     if (atom.getBonds().size() == 2) {
       extremities.add(atom);
       continue;
     }
     otherAtoms.add(atom);
   }
 }
Ejemplo n.º 2
0
  // straight Euler method computation of spring forces per timestep
  // uses a maximum speed limiter to prevent numerical problems
  // doesn't lose overall speed however, since force computation typically
  // overestimates anyway
  // but reliable and quick
  // disadvantage: bonded atom groups lose group momentum as speed limiter
  // kicks in
  // some possible alternative physics:
  // - a hard-sphere type physics, where instead of a constant timestep we
  // search for future
  // collisions between the spheres and run the sim forward to that point, and
  // recompute their
  // velocities as a result of the collision. might be promising to explore
  // for OB - but how to include
  // bonds (and dragging)?
  // - a lattice-based physics can run very fast indeed but doesn't look as
  // satisfying
  public void doTimeStep(final DraggingPoint draggingPoint, final List<Reaction> reactions) {
    // boolean is_dragging,int which_being_dragged, int mouse_x,int mouse_y
    // COMPUTE AND REACT
    // we shuffle the reactions list in order to prevent any reaction
    // artefacts, since
    // reactions are applied as they are found, and conflicting reactions
    // would only ever have
    // the first one applied, eg. with a1c1->a2c2 and x1c1->x4c4, only the
    // first version would apply
    // to any a1c1 pairs. Now each reaction has an equal chance of being
    // chosen.
    Collections.shuffle(reactions);

    // starting over for this iteration
    reactedAtoms.clear();
    // TODO the collider should not be responsible for the mangement of
    // reactions

    final float R = Atom.getAtomSize();
    final float diam = 2.0f * R;
    final float diam2 = diam * diam;

    for (int i = 0; i < atoms.size(); i++) {
      Atom a = atoms.get(i);
      // bounce off the walls
      if (a.getPhysicalPoint().getPositionX() < R) {
        a.getPhysicalPoint()
            .setSpeedX(
                a.getPhysicalPoint().getSpeedX()
                    + getForce(R - a.getPhysicalPoint().getPositionX()));
      }
      if (a.getPhysicalPoint().getPositionY() < R) {
        a.getPhysicalPoint()
            .setSpeedY(
                a.getPhysicalPoint().getSpeedY()
                    + getForce(R - a.getPhysicalPoint().getPositionY()));
      }
      if (a.getPhysicalPoint().getPositionX() > width - R) {
        a.getPhysicalPoint()
            .setSpeedX(
                a.getPhysicalPoint().getSpeedX()
                    - getForce(a.getPhysicalPoint().getPositionX() - (width - R)));
      }
      if (a.getPhysicalPoint().getPositionY() > height - R) {
        a.getPhysicalPoint()
            .setSpeedY(
                a.getPhysicalPoint().getSpeedY()
                    - getForce(a.getPhysicalPoint().getPositionY() - (height - R)));
      }
      // bounce off other atoms that are within 2R distance of this one
      // what square radius must we search for neighbours?
      final int rx = (int) Math.ceil(diam / bucket_width);
      final int ry = (int) Math.ceil(diam / bucket_height);
      // what bucket is the atom in?
      final int wx = whichBucketX(a.getPhysicalPoint().getPositionX());
      final int wy = whichBucketY(a.getPhysicalPoint().getPositionY());
      // accumulate the list of any atoms in this square radius (clamped
      // to the valid area)
      for (int x = Math.max(0, wx - rx); x <= Math.min(n_buckets_x - 1, wx + rx); x++) {
        for (int y = Math.max(0, wy - ry); y <= Math.min(n_buckets_y - 1, wy + ry); y++) {
          // add each atom that is in this bucket
          final Iterator<Integer> it = buckets.get(x).get(y).listIterator();
          while (it.hasNext()) {
            final int iOther = it.next().intValue();
            if (iOther <= i) {
              continue; // using Newton's "action&reaction" as a
            }
            // shortcut
            Atom b = atoms.get(iOther);
            if (new Point2D.Float(
                        a.getPhysicalPoint().getPositionX(), a.getPhysicalPoint().getPositionY())
                    .distanceSq(
                        new Point2D.Float(
                            b.getPhysicalPoint().getPositionX(),
                            b.getPhysicalPoint().getPositionY()))
                < diam2) {
              // this is a collision - can any reactions apply to
              // these two atoms?
              if (!a.isKiller() && !b.isKiller()) {
                for (int twice = 0;
                    twice < 2 && !reactedAtoms.contains(a) && !reactedAtoms.contains(b);
                    twice++) {
                  // try each reaction in turn
                  final Iterator<Reaction> iterator = reactions.listIterator();
                  while (iterator.hasNext()
                      && !reactedAtoms.contains(a)
                      && !reactedAtoms.contains(b)) {
                    if (iterator.next().tryOn(a, b)) {
                      reactedAtoms.add(a);
                      reactedAtoms.add(b);
                    }
                  }
                  // now swap a and b and try again
                  final Atom temp = a;
                  a = b;
                  b = temp;
                }
              } else {
                // the killer atom breaks the other atoms bonds
                // (unless other is an 'a' atom)
                if (a.isKiller()) {
                  if (b.getType() != BasicType.A) {
                    b.breakAllBonds();
                  }
                } else {
                  if (a.getType() != BasicType.A) {
                    a.breakAllBonds();
                  }
                }
              }
              // atoms bounce off other atoms
              final float sep =
                  (float)
                      new Point2D.Float(
                              a.getPhysicalPoint().getPositionX(),
                              a.getPhysicalPoint().getPositionY())
                          .distance(
                              new Point2D.Float(
                                  b.getPhysicalPoint().getPositionX(),
                                  b.getPhysicalPoint().getPositionY()));
              final float force = getForce(diam - sep);
              // push from the other atom
              final float dx =
                  force
                      * (a.getPhysicalPoint().getPositionX() - b.getPhysicalPoint().getPositionX())
                      / sep;
              final float dy =
                  force
                      * (a.getPhysicalPoint().getPositionY() - b.getPhysicalPoint().getPositionY())
                      / sep;
              a.getPhysicalPoint().setSpeedX(a.getPhysicalPoint().getSpeedX() + dx);
              a.getPhysicalPoint().setSpeedY(a.getPhysicalPoint().getSpeedY() + dy);
              b.getPhysicalPoint().setSpeedX(b.getPhysicalPoint().getSpeedX() - dx); // using
              // Newton's
              // "action&reaction"
              // as
              // a
              // shortcut
              b.getPhysicalPoint().setSpeedY(b.getPhysicalPoint().getSpeedY() - dy);
            }
          }
        }
      }
      // bonds act like springs
      final Iterator<Atom> it = a.getBonds().iterator();
      while (it.hasNext()) {
        final Atom other = it.next();
        final float sep =
            (float)
                new Point2D.Float(
                        a.getPhysicalPoint().getPositionX(), a.getPhysicalPoint().getPositionY())
                    .distance(
                        new Point2D.Float(
                            other.getPhysicalPoint().getPositionX(),
                            other.getPhysicalPoint().getPositionY()));
        final float force = getForce(sep - diam) / 4.0f; // this
        // determines
        // the bond spring
        // stiffness
        // pull towards the other atom
        final float dx =
            force
                * (other.getPhysicalPoint().getPositionX() - a.getPhysicalPoint().getPositionX())
                / sep;
        final float dy =
            force
                * (other.getPhysicalPoint().getPositionY() - a.getPhysicalPoint().getPositionY())
                / sep;
        a.getPhysicalPoint().setSpeedX(a.getPhysicalPoint().getSpeedX() + dx);
        a.getPhysicalPoint().setSpeedY(a.getPhysicalPoint().getSpeedY() + dy);
      }
      // the user can pull atoms about using the mouse
      if (draggingPoint != null && draggingPoint.getWhichBeingDragging() == i) {
        // normalise the pull vector
        float pullX = draggingPoint.getX() - a.getPhysicalPoint().getPositionX();
        float pullY = draggingPoint.getY() - a.getPhysicalPoint().getPositionY();
        final float dist = (float) Math.sqrt(pullX * pullX + pullY * pullY);
        pullX /= dist;
        pullY /= dist;
        a.getPhysicalPoint().setSpeedX(a.getPhysicalPoint().getSpeedX() + 2.0f * pullX);
        a.getPhysicalPoint().setSpeedY(a.getPhysicalPoint().getSpeedY() + 2.0f * pullY);
      }
      // limit the velocity of each atom to prevent numerical problems
      final float speed =
          (float)
              Math.sqrt(
                  a.getPhysicalPoint().getSpeedX() * a.getPhysicalPoint().getSpeedX()
                      + a.getPhysicalPoint().getSpeedY() * a.getPhysicalPoint().getSpeedY());
      if (speed > MAX_SPEED) {
        a.getPhysicalPoint().setSpeedX(a.getPhysicalPoint().getSpeedX() * MAX_SPEED / speed);
        a.getPhysicalPoint().setSpeedY(a.getPhysicalPoint().getSpeedY() * MAX_SPEED / speed);
      }
    }

    // MOVE ATOMS
    for (int i = 0; i < atoms.size(); i++) {
      final Atom a = atoms.get(i);
      if (a.isStuck()) {
        continue; // special atoms that don't move
      }

      int current_bucket_x, current_bucket_y;
      current_bucket_x = whichBucketX(a.getPhysicalPoint().getPositionX());
      current_bucket_y = whichBucketY(a.getPhysicalPoint().getPositionY());

      a.getPhysicalPoint()
          .setPositionX(
              a.getPhysicalPoint().getPositionX() + atoms.get(i).getPhysicalPoint().getSpeedX());
      a.getPhysicalPoint()
          .setPositionY(
              a.getPhysicalPoint().getPositionY() + atoms.get(i).getPhysicalPoint().getSpeedY());

      int new_bucket_x, new_bucket_y;
      new_bucket_x = whichBucketX(a.getPhysicalPoint().getPositionX());
      new_bucket_y = whichBucketY(a.getPhysicalPoint().getPositionY());

      // do we need to move the atom to a new bucket?
      if (new_bucket_x != current_bucket_x || new_bucket_y != current_bucket_y) {
        // remove the atom index from the list
        final List<Integer> list = buckets.get(current_bucket_x).get(current_bucket_y);
        final Iterator<Integer> it = list.listIterator(0);
        while (it.hasNext()) {
          if (it.next().intValue() == i) {
            it.remove();
          }
        }
        buckets.get(new_bucket_x).get(new_bucket_y).add(new Integer(i));
      }
    }
  }