void HoomdMove::addBonds()
{
// Loop over bonds and initialize them
int iSpec;
System::MoleculeIterator molIter;
Molecule::BondIterator bondIter;
for (iSpec=0; iSpec < simulation().nSpecies(); ++iSpec) {
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter) {
for (molIter->begin(bondIter); bondIter.notEnd(); ++bondIter) {
::Bond bond(bondIter->typeId(),
bondIter->atom(0).id(),
bondIter->atom(1).id());
bondDataSPtr_->addBond(bond);
}
}
}
}
/// Add particle pairs to RDF histogram.
void BondLengthDist::sample(long iStep)
{
if (isAtInterval(iStep)) {
System::MoleculeIterator molIter;
Molecule::BondIterator bondIter;
double lsq, l;
for (system().begin(speciesId_, molIter); molIter.notEnd(); ++molIter) {
for (molIter->begin(bondIter); bondIter.notEnd(); ++bondIter) {
lsq = system().boundary().distanceSq( bondIter->atom(0).position(),
bondIter->atom(1).position());
l = sqrt(lsq);
accumulator_.sample(l);
}
}
}
}
/*
* Evaluate Rosenbluth weight, and add to accumulator.
*/
void McChemicalPotential::sample(long iStep)
{
if (isAtInterval(iStep)) {
Species* speciesPtr;
Molecule* molPtr;
Molecule::BondIterator bondIter;
Atom* endPtr;
double w;
double rosenbluth = 1;
double de;
double e = 0;
speciesPtr = &(simulation().species(speciesId_));
// Pop a new molecule off the species reservoir
molPtr = &(speciesPtr->reservoir().pop());
system().addMolecule(*molPtr);
// Loop over molecule growth trials
for (int i = 0; i < nMoleculeTrial_; i++) {
// Pick a random position for the first atom
endPtr = &molPtr->atom(0);
boundary().randomPosition(random(), endPtr->position());
e = system().pairPotential().atomEnergy(*endPtr);
rosenbluth = boltzmann(e);
system().pairPotential().addAtom(*endPtr);
for (molPtr->begin(bondIter); bondIter.notEnd(); ++bondIter) {
addEndAtom(&(bondIter->atom(1)), &(bondIter->atom(0)), bondIter->typeId(), w, de);
e += de;
rosenbluth *= w;
system().pairPotential().addAtom(bondIter->atom(1));
}
rosenbluth = rosenbluth / pow(nTrial_,molPtr->nAtom()-1);
accumulator_.sample(rosenbluth, outputFile_);
system().pairPotential().deleteAtom(*endPtr);
for (molPtr->begin(bondIter); bondIter.notEnd(); ++bondIter) {
system().pairPotential().deleteAtom(bondIter->atom(1));
}
}
// Return additional molecule to reservoir
system().removeMolecule(*molPtr);
speciesPtr->reservoir().push(*molPtr);
}
}