/*
* Pop and process the next molecule on the workStack (private).
*/
void ClusterIdentifier::processNextMolecule(Cluster& cluster)
{
CellList::NeighborArray neighborArray;
Molecule::AtomIterator atomIter;
ClusterLink* thisLinkPtr;
ClusterLink* otherLinkPtr;
Atom* otherAtomPtr;
Boundary& boundary = system().boundary();
double cutoffSq = cutoff_*cutoff_;
double rsq;
int thisMolId, otherMolId, otherClusterId;
// Pop this molecule off the stack
thisLinkPtr = &workStack_.pop();
thisMolId = thisLinkPtr->molecule().id();
if (thisLinkPtr->clusterId() != cluster.id()) {
UTIL_THROW("Top ClusterLink not marked with this cluster id");
}
/*
* Loop over atoms of this molecule.
* For each atom of type atomTypeId_, find neighboring molecules.
* Add each new neighbor to the cluster, and to the workStack.
*/
thisLinkPtr->molecule().begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
if (atomIter->typeId() == atomTypeId_) {
cellList_.getNeighbors(atomIter->position(), neighborArray);
for (int i = 0; i < neighborArray.size(); i++) {
otherAtomPtr = neighborArray[i];
otherMolId = otherAtomPtr->molecule().id();
if (otherMolId != thisMolId) {
rsq = boundary.distanceSq(atomIter->position(),
otherAtomPtr->position());
if (rsq < cutoffSq) {
otherLinkPtr = &(links_[otherMolId]);
assert(&otherLinkPtr->molecule() ==
&otherAtomPtr->molecule());
otherClusterId = otherLinkPtr->clusterId();
if (otherClusterId == -1) {
cluster.addLink(*otherLinkPtr);
workStack_.push(*otherLinkPtr);
} else
if (otherClusterId != cluster.id()) {
UTIL_THROW("Cluster Clash!");
}
}
}
} // neighbor atoms
}
} // atoms
}
/*
* Identify all clusters in the system.
*/
void ClusterIdentifier::identifyClusters()
{
// Initialize all data structures:
// Setup a grid of empty cells
cellList_.setup(system().boundary(), cutoff_);
// Clear clusters array and all links
clusters_.clear();
for (int i = 0; i < links_.capacity(); ++i) {
links_[i].clear();
}
// Build the cellList, associate Molecule with ClusterLink.
// Iterate over molecules of species speciesId_
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
system().begin(speciesId_, molIter);
for ( ; molIter.notEnd(); ++molIter) {
// Associate this Molecule with a ClusterLink
links_[molIter->id()].setMolecule(*molIter.get());
// Add atoms of type = atomTypeId_ to the CellList
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
if (atomIter->typeId() == atomTypeId_) {
system().boundary().shift(atomIter->position());
cellList_.addAtom(*atomIter);
}
}
}
// Identify all clusters
Cluster* clusterPtr;
ClusterLink* linkPtr;
int clusterId = 0;
system().begin(speciesId_, molIter);
for ( ; molIter.notEnd(); ++molIter) {
// Find the link with same index as this molecule
linkPtr = &(links_[molIter->id()]);
assert (&(linkPtr->molecule()) == molIter.get());
// If this link is not in a cluster, begin a new cluster
if (linkPtr->clusterId() == -1) {
// Add a new empty cluster to clusters_ array
clusters_.resize(clusterId+1);
clusterPtr = &clusters_[clusterId];
clusterPtr->clear();
clusterPtr->setId(clusterId);
// Identify molecules in this cluster
clusterPtr->addLink(*linkPtr);
workStack_.push(*linkPtr);
while (workStack_.size() > 0) {
processNextMolecule(*clusterPtr);
}
clusterId++;
}
}
// Validity check - throws exception on failure.
isValid();
}
