/*
* 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();
}
/*
* Evaluate end-to-end vectors of all chains, add to ensemble.
*/
void ClustersDynamics::sample(long iStep)
{ if (isAtInterval(iStep)) {
newClustersPtr_->sample(iStep);
if (iStep == 0) {
oldClustersPtr_->sample(iStep);
}
int clustersCorrelations_[newClustersPtr_->clusterLengths_.size()][oldClustersPtr_->clusterLengths_.size()];
for (int i = 0; i < newClustersPtr_->clusterLengths_.size(); i++) {
for (int j = 0; j < oldClustersPtr_->clusterLengths_.size(); j++) {
clustersCorrelations_[i][j] = 0;
}
}
System::MoleculeIterator molIter;
for (system().begin(speciesId_, molIter); molIter.notEnd(); ++molIter) {
clustersCorrelations_[newClustersPtr_->clusters_[molIter->id()].clusterId_][oldClustersPtr_->clusters_[molIter->id()].clusterId_] += 1 ;
}
bool usedIds_[newClustersPtr_->clusterLengths_.size()];
int idConversions_[newClustersPtr_->clusterLengths_.size()];
for (int i = 0; i < newClustersPtr_->clusterLengths_.size(); i++) {
usedIds_[i] = false;
idConversions_[i] = 0;
}
int id_ = 0;
for (int i = 0; i < newClustersPtr_->clusterLengths_.size(); i++) {
for (int j = 0; j < oldClustersPtr_->clusterLengths_.size(); j++) {
//this only works if the criterion > 50%
if (clustersCorrelations_[i][j] > criterion_ * oldClustersPtr_->clusterLengths_[i]) id_ = i;
}
usedIds_[id_] = true;
idConversions_[i] = id_;
}
int usedIdCounter_ = 0;
for (int i = 0; i < newClustersPtr_->clusterLengths_.size(); i++) {
if (idConversions_[i] == 0) {
while (usedIds_[usedIdCounter_] == true) usedIdCounter_++;
idConversions_[i] = usedIdCounter_;
usedIds_[usedIdCounter_] = true;
}
}
/* for (system().begin(speciesId_, molIter); molIter.notEnd(); ++molIter) {
newClustersPtr_->clusters_[molIter->id()].clusterId_ = idConversions_[newClustersPtr_->clusters_[molIter->id()].clusterId_];
} */
std::string fileName;
fileName = outputFileName();
fileName += toString(iStep);
fileName += ".dynamics";
fileMaster().openOutputFile(fileName, outputFile_);
for (int i = 0; i < newClustersPtr_->clusterLengths_.size(); i++) {
outputFile_<<"<"<< i <<">"<<"("<<newClustersPtr_->clusterLengths_[i]<<") = ";
for (int j=0; j < oldClustersPtr_->clusterLengths_.size(); j++) {
if (clustersCorrelations_[i][j] != 0){
outputFile_<<"<"<< j <<">["<<oldClustersPtr_->clusterLengths_[j]<<"]("<<clustersCorrelations_[i][j]<<") ";
}
}
outputFile_<<"\n";
}
outputFile_.close();
ClustersFinder *tmp = oldClustersPtr_;
oldClustersPtr_ = &(*newClustersPtr_);
newClustersPtr_ = &(*tmp);
}
}