/*
* 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
}
/*
* Evaluate external energy, and add to ensemble.
*/
void McExternalEnergyAverage::sample(long iStep)
{
if (!isAtInterval(iStep)) return;
double energy = 0.0;
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
energy += system().externalPotential().energy(atomIter->position(), atomIter->typeId());
}
}
}
accumulator_.sample(energy, outputFile_);
}
/*
* 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();
}
/*
* Verlet MD NVE integrator step
*
* This method implements the algorithm:
*
* vm(n) = v(n) + 0.5*a(n)*dt
* x(n+1) = x(n) + vm(n)*dt
*
* calculate acceleration a(n+1)
*
* v(n+1) = vm(n) + 0.5*a(n+1)*dt
*
* where x is position, v is velocity, and a is acceleration.
*/
void NveVvIntegrator::step()
{
Vector dv;
Vector dr;
System::MoleculeIterator molIter;
double prefactor;
int iSpecies, nSpecies;
nSpecies = simulation().nSpecies();
// 1st half velocity Verlet, loop over atoms
#if USE_ITERATOR
Molecule::AtomIterator atomIter;
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
dr.multiply(atomIter->velocity(), dt_);
atomIter->position() += dr;
}
}
}
#else
Atom* atomPtr;
int ia;
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (ia=0; ia < molIter->nAtom(); ++ia) {
atomPtr = &molIter->atom(ia);
prefactor = prefactors_[atomPtr->typeId()];
dv.multiply(atomPtr->force(), prefactor);
atomPtr->velocity() += dv;
dr.multiply(atomPtr->velocity(), dt_);
atomPtr->position() += dr;
}
}
}
#endif
system().calculateForces();
// 2nd half velocity Verlet, loop over atoms
#if USE_ITERATOR
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
}
}
}
#else
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter)
{
for (ia=0; ia < molIter->nAtom(); ++ia) {
atomPtr = &molIter->atom(ia);
prefactor = prefactors_[atomPtr->typeId()];
dv.multiply(atomPtr->force(), prefactor);
atomPtr->velocity() += dv;
}
}
}
#endif
#ifndef INTER_NOPAIR
if (!system().pairPotential().isPairListCurrent()) {
system().pairPotential().buildPairList();
}
#endif
}
/**
* Generate random molecules
*/
void Linear::generateMolecules(int nMolecule,
DArray<double> exclusionRadius, System& system,
BondPotential *bondPotentialPtr, const Boundary &boundary)
{
int iMol;
// Set up a cell list with twice the maxium exclusion radius as the
// cell size
double maxExclusionRadius = 0.0;
for (int iType = 0; iType < system.simulation().nAtomType(); iType++) {
if (exclusionRadius[iType] > maxExclusionRadius)
maxExclusionRadius = exclusionRadius[iType];
}
// the minimum cell size is twice the maxExclusionRadius,
// but to save memory, we take 2 times that value
CellList cellList;
cellList.allocate(system.simulation().atomCapacity(),
boundary, 2.0*2.0*maxExclusionRadius);
if (nMolecule > capacity())
UTIL_THROW("nMolecule > Species.capacity()!");
Simulation& sim = system.simulation();
for (iMol = 0; iMol < nMolecule; ++iMol) {
// Add a new molecule to the system
Molecule &newMolecule= sim.getMolecule(id());
system.addMolecule(newMolecule);
// Try placing atoms
bool moleculeHasBeenPlaced = false;
for (int iAttempt = 0; iAttempt< maxPlacementAttempts_; iAttempt++) {
// Place first atom
Vector pos;
system.boundary().randomPosition(system.simulation().random(),pos);
Atom &thisAtom = newMolecule.atom(0);
// check if the first atom can be placed at the new position
CellList::NeighborArray neighbors;
cellList.getNeighbors(pos, neighbors);
int nNeighbor = neighbors.size();
bool canBePlaced = true;
for (int j = 0; j < nNeighbor; ++j) {
Atom *jAtomPtr = neighbors[j];
double r = sqrt(system.boundary().distanceSq(
jAtomPtr->position(), pos));
if (r < (exclusionRadius[thisAtom.typeId()] +
exclusionRadius[jAtomPtr->typeId()])) {
canBePlaced = false;
break;
}
}
if (canBePlaced) {
thisAtom.position() = pos;
cellList.addAtom(thisAtom);
// Try to recursively place other atoms
if (tryPlaceAtom(newMolecule, 0, exclusionRadius, system,
cellList, bondPotentialPtr, system.boundary())) {
moleculeHasBeenPlaced = true;
break;
} else {
cellList.deleteAtom(thisAtom);
}
}
}
if (! moleculeHasBeenPlaced) {
std::ostringstream oss;
oss << "Failed to place molecule " << newMolecule.id();
UTIL_THROW(oss.str().c_str());
}
}
#if 0
// Check
for (int iMol =0; iMol < nMolecule; ++iMol) {
Molecule::AtomIterator atomIter;
system.molecule(id(),iMol).begin(atomIter);
for (; atomIter.notEnd(); ++atomIter) {
for (int jMol =0; jMol < nMolecule; ++jMol) {
Molecule::AtomIterator atomIter2;
system.molecule(id(),jMol).begin(atomIter2);
for (; atomIter2.notEnd(); ++atomIter2 ) {
if (atomIter2->id() != atomIter->id()) {
double r = sqrt(boundary.distanceSq(
atomIter->position(),atomIter2->position()));
if (r < (exclusionRadius[atomIter->typeId()]+
exclusionRadius[atomIter2->typeId()])) {
std::cout << r << std::endl;
UTIL_THROW("ERROR");
}
}
}
}
}
}
#endif
}
/*
* Nose-Hoover integrator step.
*
* This implements a reversible Velocity-Verlet MD NVT integrator step.
*
* Reference: Winkler, Kraus, and Reineker, J. Chem. Phys. 102, 9018 (1995).
*/
void NvtNhIntegrator::step()
{
Vector dv;
Vector dr;
System::MoleculeIterator molIter;
double dtHalf = 0.5*dt_;
double prefactor;
double factor;
Molecule::AtomIterator atomIter;
int iSpecies, nSpecies;
int nAtom;
T_target_ = energyEnsemblePtr_->temperature();
nSpecies = simulation().nSpecies();
nAtom = system().nAtom();
factor = exp(-dtHalf*(xi_ + xiDot_*dtHalf));
// 1st half velocity Verlet, loop over atoms
for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
molIter->begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
atomIter->velocity() *= factor;
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
//dv.multiply(atomIter->force(), dtHalf);
atomIter->velocity() += dv;
dr.multiply(atomIter->velocity(), dt_);
atomIter->position() += dr;
}
}
}
// First half of update of xi_
xi_ += xiDot_*dtHalf;
#ifndef INTER_NOPAIR
// Rebuild the pair list if necessary
if (!system().pairPotential().isPairListCurrent()) {
system().pairPotential().buildPairList();
}
#endif
system().calculateForces();
// 2nd half velocity Verlet, loop over atoms
for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
prefactor = prefactors_[atomIter->typeId()];
dv.multiply(atomIter->force(), prefactor);
atomIter->velocity() += dv;
atomIter->velocity() *=factor;
}
}
}
// Update xiDot and complete update of xi_
T_kinetic_ = system().kineticEnergy()*2.0/double(3*nAtom);
xiDot_ = (T_kinetic_/T_target_ -1.0)*nuT_*nuT_;
xi_ += xiDot_*dtHalf;
}
/*
* Generate, attempt and accept or reject a Hybrid MD/MC move.
*/
bool HoomdMove::move()
{
if ((!HoomdIsInitialized_) || moleculeSetHasChanged_) {
initSimulation();
moleculeSetHasChanged_ = false;
}
// We need to create the Integrator every time since we are starting
// with new coordinates, velocities etc.
// this does not seem to incur a significant performance decrease
createIntegrator();
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
int nSpec = simulation().nSpecies();
// Increment counter for attempted moves
incrementNAttempt();
double oldEnergy, newEnergy;
{
// Copy atom coordinates into HOOMD
ArrayHandle<Scalar4> h_pos(particleDataSPtr_->getPositions(), access_location::host, access_mode::readwrite);
ArrayHandle<Scalar4> h_vel(particleDataSPtr_->getVelocities(), access_location::host, access_mode::readwrite);
ArrayHandle<unsigned int> h_tag(particleDataSPtr_->getTags(), access_location::host, access_mode::readwrite);
ArrayHandle<unsigned int> h_rtag(particleDataSPtr_->getRTags(), access_location::host, access_mode::readwrite);
for (int iSpec =0; iSpec < nSpec; ++iSpec) {
system().begin(iSpec, molIter);
for ( ; molIter.notEnd(); ++ molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
unsigned int idx = (unsigned int) atomIter->id();
Vector& pos = atomIter->position();
h_pos.data[idx].x = pos[0] - lengths_[0]/2.;
h_pos.data[idx].y = pos[1] - lengths_[1]/2.;
h_pos.data[idx].z = pos[2] - lengths_[2]/2.;
int type = atomIter->typeId();
h_vel.data[idx].w = simulation().atomType(type).mass();
h_pos.data[idx].w = __int_as_scalar(type);
h_tag.data[idx] = idx;
h_rtag.data[idx] = idx;
}
}
}
// Generate random velocities
generateRandomVelocities(h_vel);
}
// Notify that the particle order has changed
particleDataSPtr_->notifyParticleSort();
// Initialize integrator (calculate forces and potential energy for step 0)
integratorSPtr_->prepRun(0);
// Calculate oldEnergy
thermoSPtr_->compute(0);
oldEnergy = thermoSPtr_->getLogValue("kinetic_energy",0);
oldEnergy += thermoSPtr_->getLogValue("potential_energy",0);
// Integrate nStep_ steps forward
for (int iStep = 0; iStep < nStep_; ++iStep) {
integratorSPtr_->update(iStep);
// do we need to sort the particles?
// do not sort at time step 0 to speed up short runs
if (! (iStep % sorterPeriod_) && iStep)
sorterSPtr_->update(iStep);
}
// Calculate new energy
thermoSPtr_->compute(nStep_);
newEnergy = thermoSPtr_->getLogValue("kinetic_energy",nStep_);
newEnergy += thermoSPtr_->getLogValue("potential_energy",nStep_);
// Decide whether to accept or reject
bool accept = random().metropolis( boltzmann(newEnergy-oldEnergy) );
if (accept) {
// read back integrated positions
ArrayHandle<Scalar4> h_pos(particleDataSPtr_->getPositions(), access_location::host, access_mode::read);
ArrayHandle<Scalar4> h_vel(particleDataSPtr_->getVelocities(), access_location::host, access_mode::read);
ArrayHandle<unsigned int> h_tag(particleDataSPtr_->getTags(), access_location::host, access_mode::read);
ArrayHandle<unsigned int> h_rtag(particleDataSPtr_->getRTags(), access_location::host, access_mode::read);
for (int iSpec = 0; iSpec < nSpec; ++iSpec) {
system().begin(iSpec, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
unsigned int idx = h_rtag.data[atomIter->id()];
atomIter->position() = Vector(h_pos.data[idx].x+lengths_[0]/2.,
h_pos.data[idx].y+lengths_[1]/2.,
h_pos.data[idx].z+lengths_[2]/2.);
}
}
}
system().pairPotential().buildCellList();
incrementNAccept();
} else {
// not accepted, do nothing
}
return accept;
}