@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);
}
}
// 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));
}
}
}