/*
* Build the PairList.
*/
void MdPairPotential::buildPairList()
{
// Recalculate the grid for the internal CellList
pairList_.makeGrid(boundary());
// Clear all atoms from the internal CellList
pairList_.clear();
// Add every atom in this System to the CellList
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
for (int iSpec=0; iSpec < simulation().nSpecies(); ++iSpec) {
for (begin(iSpec, molIter); molIter.notEnd(); ++molIter) {
molIter->begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
#ifdef MCMD_SHIFT
boundary().shift(atomIter->position(), atomIter->shift());
#else
boundary().shift(atomIter->position());
#endif
pairList_.addAtom(*atomIter);
}
}
}
// Use the completed CellList to build the PairList
pairList_.build(boundary());
}
/*
* 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_);
}
/*
* Build the CellList.
*/
void McPairPotential::buildCellList()
{
// Set up a grid of empty cells.
cellList_.setup(boundary(), maxPairCutoff());
// Add all atoms to cellList_
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
for (int iSpec=0; iSpec < simulation().nSpecies(); ++iSpec) {
for (begin(iSpec, molIter); molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
boundary().shift(atomIter->position());
cellList_.addAtom(*atomIter);
}
}
}
}
/*
* 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, attempt and accept or reject a Hybrid MD/MC move.
*/
bool HybridNphMdMove::move()
{
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
double oldEnergy, newEnergy;
int iSpec;
int nSpec = simulation().nSpecies();
bool accept;
if (nphIntegratorPtr_ == NULL) {
UTIL_THROW("null integrator pointer");
}
// Increment counter for attempted moves
incrementNAttempt();
// Store old boundary lengths.
Vector oldLengths = system().boundary().lengths();
// Store old atom positions in oldPositions_ array.
for (iSpec = 0; iSpec < nSpec; ++iSpec) {
mdSystemPtr_->begin(iSpec, molIter);
for ( ; molIter.notEnd(); ++molIter) {
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
oldPositions_[atomIter->id()] = atomIter->position();
}
}
}
// Initialize MdSystem
#ifndef INTER_NOPAIR
mdSystemPtr_->pairPotential().buildPairList();
#endif
mdSystemPtr_->calculateForces();
mdSystemPtr_->setBoltzmannVelocities(energyEnsemble().temperature());
nphIntegratorPtr_->setup();
// generate integrator variables from a Gaussian distribution
Random& random = simulation().random();
double temp = system().energyEnsemble().temperature();
double volume = system().boundary().volume();
if (mode_ == Cubic) {
// one degree of freedom
// barostat_energy = 1/2 (1/W) eta_x^2
double sigma = sqrt(temp/barostatMass_);
nphIntegratorPtr_->setEta(0, sigma*random.gaussian());
} else if (mode_ == Tetragonal) {
// two degrees of freedom
// barostat_energy = 1/2 (1/W) eta_x^2 + 1/2 (1/(2W)) eta_y^2
double sigma1 = sqrt(temp/barostatMass_);
nphIntegratorPtr_->setEta(0, sigma1*random.gaussian());
double sigma2 = sqrt(temp/barostatMass_/2.0);
nphIntegratorPtr_->setEta(1, sigma2*random.gaussian());
} else if (mode_ == Orthorhombic) {
// three degrees of freedom
// barostat_energy = 1/2 (1/W) (eta_x^2 + eta_y^2 + eta_z^2)
double sigma = sqrt(temp/barostatMass_);
nphIntegratorPtr_->setEta(0, sigma*random.gaussian());
nphIntegratorPtr_->setEta(1, sigma*random.gaussian());
nphIntegratorPtr_->setEta(2, sigma*random.gaussian());
}
// Store old energy
oldEnergy = mdSystemPtr_->potentialEnergy();
oldEnergy += mdSystemPtr_->kineticEnergy();
oldEnergy += system().boundaryEnsemble().pressure()*volume;
oldEnergy += nphIntegratorPtr_->barostatEnergy();
// Run a short MD simulation
for (int iStep = 0; iStep < nStep_; ++iStep) {
nphIntegratorPtr_->step();
}
volume = system().boundary().volume();
// Calculate new energy
newEnergy = mdSystemPtr_->potentialEnergy();
newEnergy += mdSystemPtr_->kineticEnergy();
newEnergy += system().boundaryEnsemble().pressure()*volume;
newEnergy += nphIntegratorPtr_->barostatEnergy();
// Decide whether to accept or reject
accept = random.metropolis( boltzmann(newEnergy-oldEnergy) );
// Accept move
if (accept) {
#ifndef INTER_NOPAIR
// Rebuild the McSystem cellList using the new positions.
system().pairPotential().buildCellList();
#endif
// Increment counter for the number of accepted moves.
incrementNAccept();
} else {
// Restore old boundary lengths
system().boundary().setOrthorhombic(oldLengths);
// Restore old atom positions
for (iSpec = 0; iSpec < nSpec; ++iSpec) {
mdSystemPtr_->begin(iSpec, molIter);
for ( ; molIter.notEnd(); ++molIter) {
molIter->begin(atomIter);
for ( ; atomIter.notEnd(); ++atomIter) {
atomIter->position() = oldPositions_[atomIter->id()];
}
}
}
}
return accept;
}
/**
* 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;
}
/*
* Perform replica exchange move.
*/
bool ReplicaMove::move()
{
MPI::Request request[4];
MPI::Status status;
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
int iA;
int recvPt, sendPt;
DArray<int> permutation;
permutation.allocate(nProcs_);
// Gather all derivatives of the perturbation Hamiltonians and parameters on processor with rank 0
DArray<double> myDerivatives;
myDerivatives.allocate(nParameters_);
DArray<double> myParameters;
myParameters.allocate(nParameters_);
for (int i=0; i< nParameters_; i++) {
myDerivatives[i] = system().perturbation().derivative(i);
myParameters[i] = system().perturbation().parameter(i);
}
int size = 0;
size += memorySize(myDerivatives);
size += memorySize(myParameters);
if (myId_ != 0) {
MemoryOArchive sendCurrent;
sendCurrent.allocate(size);
sendCurrent << myDerivatives;
sendCurrent << myParameters;
sendCurrent.send(*communicatorPtr_, 0);
} else {
DArray< DArray<double> > allDerivatives;
DArray< DArray<double> > allParameters;
allDerivatives.allocate(nProcs_);
allParameters.allocate(nProcs_);
allDerivatives[0].allocate(nParameters_);
allDerivatives[0] = myDerivatives;
allParameters[0].allocate(nParameters_);
allParameters[0] = myParameters;
for (int i = 1; i<nProcs_; i++) {
MemoryIArchive recvPartner;
recvPartner.allocate(size);
recvPartner.recv(*communicatorPtr_, i);
allDerivatives[i].allocate(nParameters_);
allParameters[i].allocate(nParameters_);
recvPartner >> allDerivatives[i];
recvPartner >> allParameters[i];
}
// Now we have the complete matrix U_ij = u_i(x_j), permutate nsampling steps according
// to acceptance criterium
// start with identity permutation
for (int i = 0; i < nProcs_; i++)
permutation[i] = i;
for (int n =0; n < nSampling_; n++) {
swapAttempt_++;
// choose a pair i,j, i!= j at random
int i = system().simulation().random().uniformInt(0,nProcs_);
int j = system().simulation().random().uniformInt(0,nProcs_-1);
if (i<=j) j++;
// apply acceptance criterium
double weight = 0;
for (int k = 0; k < nParameters_; k++) {
double deltaDerivative = allDerivatives[i][k] - allDerivatives[j][k];
// the permutations operate on the states (the perturbation parameters)
weight += (allParameters[permutation[j]][k] - allParameters[permutation[i]][k])*deltaDerivative;
}
double exponential = exp(-weight);
int accept = system().simulation().random(). metropolis(exponential) ? 1 : 0;
if (accept) {
swapAccept_++;
// swap states of pair i,j
int tmp = permutation[i];
permutation[i] = permutation[j];
permutation[j] = tmp;
}
}
// send exchange partner information to all other processors
for (int i = 0; i < nProcs_; i++) {
if (i != 0)
communicatorPtr_->Send(&permutation[i], 1, MPI::INT, i, 0);
else
sendPt = permutation[i];
if (permutation[i] != 0)
communicatorPtr_->Send(&i, 1, MPI::INT, permutation[i], 1);
else
recvPt = i;
}
}
if (myId_ != 0) {
// partner id to receive from
communicatorPtr_->Recv(&sendPt, 1, MPI::INT, 0, 0);
// partner id to send to
communicatorPtr_->Recv(&recvPt, 1, MPI::INT, 0, 1);
}
if (recvPt == myId_ || sendPt == myId_) {
// no exchange necessary
outputFile_ << sendPt << std::endl;
return true;
}
assert(recvPt != myId_ && sendPt != myId_);
Vector myBoundary;
myBoundary = system().boundary().lengths();
Vector ptBoundary;
// Accomodate new boundary dimensions.
request[0] = communicatorPtr_->Irecv(&ptBoundary, 1,
MpiTraits<Vector>::type, recvPt, 1);
// Send old boundary dimensions.
request[1] = communicatorPtr_->Isend(&myBoundary, 1,
MpiTraits<Vector>::type, sendPt, 1);
request[0].Wait();
request[1].Wait();
system().boundary().setOrthorhombic(ptBoundary);
// Pack atomic positions and types.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
myPositionPtr_[iA] = atomIter->position();
iA++;
}
}
}
// Accomodate new configuration.
request[2] = communicatorPtr_->Irecv(ptPositionPtr_, iA,
MpiTraits<Vector>::type, recvPt, 2);
// Send old configuration.
request[3] = communicatorPtr_->Isend(myPositionPtr_, iA,
MpiTraits<Vector>::type, sendPt, 2);
request[2].Wait();
request[3].Wait();
// Adopt the new atomic positions.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter){
atomIter->position() = ptPositionPtr_[iA];
++iA;
}
}
}
// Notify component observers.
sendRecvPair partners;
partners[0] = sendPt;
partners[1] = recvPt;
Notifier<sendRecvPair>::notifyObservers(partners);
// Log information about exchange partner to file
outputFile_ << sendPt << std::endl;
return true;
}
/*
* 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;
}
/*
* Empty implementation, to be filled by derived classes.
*/
bool ReplicaMove::move()
{
MPI::Request request[8];
MPI::Status status;
double ptParam, myWeight, ptWeight;
int isLeft, iAccept, myPort, ptPort;
System::MoleculeIterator molIter;
Molecule::AtomIterator atomPtr;
int iA;
// Default value for idle processor
isLeft = -1;
iAccept = 0;
// Idenfity active processor and its parter ID; left one has smaller ID.
if ((myId_ + xFlag_)%2 == 0 && myId_ < nProcs_-1) {
isLeft = 1;
ptId_ = myId_ + 1;
} else if ((myId_ + xFlag_)%2 == 1 && myId_ > 0) {
isLeft = 0;
ptId_ = myId_ - 1;
}
// Start to talk with partner
if (isLeft == 1 || isLeft == 0) {
// Set the port value for message tag
myPort = myId_%2;
ptPort = ptId_%2;
// Update accumulator
repxAttempt_[isLeft] += 1;
// Exchange coupling parameters with partner
request[0] = communicatorPtr_->Irecv(&ptParam, 1, MPI::DOUBLE, ptId_,
TagParam[ptPort]);
request[1] = communicatorPtr_->Isend(&myParam_, 1, MPI::DOUBLE, ptId_,
TagParam[myPort]);
// Synchronizing
request[0].Wait();
request[1].Wait();
// Evaluating energy change.
myWeight = system().perturbation().difference(ptParam);
// Collect tempering weights and make decision
if (isLeft == 1) {
// Receive energy difference from the right box
request[2] = communicatorPtr_->Irecv(&ptWeight, 1, MPI::DOUBLE,
ptId_, TagDecision[ptPort]);
request[2].Wait();
// Metropolis test
iAccept = system().simulation().random().
metropolis(exp(-myWeight - ptWeight)) ? 1 : 0;
// Output the two weights and the metropolis of their summation.
// energyFile_ << setw(10) << myWeight << setw(10)
// << ptWeight << setw(2) << iAccept << std::endl;
// Send decision to the right box
request[3] = communicatorPtr_->Isend(&iAccept, 1, MPI::INT,
ptId_, TagDecision[myPort]);
request[3].Wait();
} else {
// Send energy difference to the left box
request[2] = communicatorPtr_->Isend(&myWeight, 1, MPI::DOUBLE,
ptId_, TagDecision[myPort]);
request[2].Wait();
// Receive decision from the left box
request[3] = communicatorPtr_->Irecv(&iAccept, 1, MPI::INT,
ptId_, TagDecision[ptPort]);
request[3].Wait();
}
// Exchange particle configurations if the move is accepted
if (iAccept == 1) {
// Update accumulator
repxAccept_[isLeft] += 1;
// Pack atomic positions and types.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); !molIter.isEnd(); ++molIter){
for (molIter->begin(atomPtr); !atomPtr.isEnd(); ++atomPtr) {
myPositionPtr_[iA] = atomPtr->position();
iA++;
}
}
}
// Accomodate new configuration.
request[4] = communicatorPtr_->Irecv(ptPositionPtr_, iA,
MpiTraits<Vector>::type, ptId_, TagConfig[ptPort]);
// Send old configuration.
request[5] = communicatorPtr_->Isend(myPositionPtr_, iA,
MpiTraits<Vector>::type, ptId_, TagConfig[myPort]);
request[4].Wait();
request[5].Wait();
// Adopt the new atomic positions.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); !molIter.isEnd(); ++molIter){
for (molIter->begin(atomPtr); !atomPtr.isEnd(); ++atomPtr) {
atomPtr->position() = ptPositionPtr_[iA];
++iA;
}
}
}
// Notify component observers.
//notifyObservers(ptId_);
Notifier<int>::notifyObservers(ptId_);
} else {
}
}
// Output results needed to build exchange profile.
outputFile_ << ((isLeft != -1 && iAccept == 1) ? ptId_ : myId_)
<< std::endl;
// Flip the value of xFlag_ before exit.
xFlag_ = (xFlag_ == 0 ? 1 : 0);
return (iAccept == 1 ? true : false);
}
/*
* Perform replica exchange move.
*/
bool ReplicaMove::move()
{
MPI::Request request[8];
MPI::Status status;
double myWeight, ptWeight, exponential;
int isLeft, iAccept, myPort, ptPort;
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
int iA;
// Default value for no replica exchange
isLeft = -1;
iAccept = 0;
if ((myId_ < nProcs_ - 1) && (stepCount_ >= myId_) &&
((stepCount_ - myId_) % (nProcs_ - 1) ==0)) {
// we are exchanging with processor myId_ + 1
isLeft = 1;
ptId_ = myId_ + 1;
} else if ((myId_ > 0) && (stepCount_ >= myId_ - 1) &&
((stepCount_ - (myId_ - 1)) % (nProcs_ -1 ) == 0)) {
// we are exchanging with processor myId_ - 1
isLeft = 0;
ptId_ = myId_ - 1;
}
if (isLeft == 0 || isLeft == 1) {
// Set the port value for message tag
myPort = myId_%2;
ptPort = ptId_%2;
// Update accumulator
repxAttempt_[isLeft] += 1;
// Exchange coupling parameters with partner
for (int i = 0; i < nParameters_; ++i) {
request[0] = communicatorPtr_->Irecv(&ptParam_[i], 1, MPI::DOUBLE, ptId_,
TagParam[ptPort]);
request[1] = communicatorPtr_->Isend(&myParam_[i], 1, MPI::DOUBLE, ptId_,
TagParam[myPort]);
// Synchronizing
request[0].Wait();
request[1].Wait();
}
myWeight = system().perturbation().difference(ptParam_);
// Collect tempering weights and make decision
if (isLeft == 1) {
// Receive energy difference from the right box
request[2] = communicatorPtr_->Irecv(&ptWeight, 1, MPI::DOUBLE,
ptId_, TagDecision[ptPort]);
request[2].Wait();
exponential = exp(-myWeight - ptWeight);
} else {
// Send energy difference to the left box
request[2] = communicatorPtr_->Isend(&myWeight, 1, MPI::DOUBLE,
ptId_, TagDecision[myPort]);
request[2].Wait();
}
// Collect tempering weights and make decision
if (isLeft == 1) {
// Metropolis test
iAccept = system().simulation().random().
metropolis(exponential) ? 1 : 0;
// Send decision to the right box
request[3] = communicatorPtr_->Isend(&iAccept, 1, MPI::INT,
ptId_, TagDecision[myPort]);
request[3].Wait();
} else {
// Receive decision from the left box
request[3] = communicatorPtr_->Irecv(&iAccept, 1, MPI::INT,
ptId_, TagDecision[ptPort]);
request[3].Wait();
}
// Exchange particle configurations if the move is accepted
if (iAccept == 1) {
// Update accumulator
repxAccept_[isLeft] += 1;
Vector myBoundary;
myBoundary = system().boundary().lengths();
Vector ptBoundary;
// Accomodate new boundary dimensions.
request[4] = communicatorPtr_->Irecv(&ptBoundary, 1,
MpiTraits<Vector>::type, ptId_, TagConfig[ptPort]);
// Send old boundary dimensions.
request[5] = communicatorPtr_->Isend(&myBoundary, 1,
MpiTraits<Vector>::type, ptId_, TagConfig[myPort]);
request[4].Wait();
request[5].Wait();
system().boundary().setOrthorhombic(ptBoundary);
// Pack atomic positions and types.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
myPositionPtr_[iA] = atomIter->position();
iA++;
}
}
}
// Accomodate new configuration.
request[6] = communicatorPtr_->Irecv(ptPositionPtr_, iA,
MpiTraits<Vector>::type, ptId_, TagConfig[ptPort]);
// Send old configuration.
request[7] = communicatorPtr_->Isend(myPositionPtr_, iA,
MpiTraits<Vector>::type, ptId_, TagConfig[myPort]);
request[6].Wait();
request[7].Wait();
// Adopt the new atomic positions.
iA = 0;
for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter){
atomIter->position() = ptPositionPtr_[iA];
++iA;
}
}
}
// Notify component observers.
//notifyObservers(ptId_);
Notifier<int>::notifyObservers(ptId_);
} else {
// the move was not accepted, do nothing
}
}
// Output results needed to build exchange profile.
if (isLeft == -1) {
outputFile_ << "n" << std::endl;
} else if ( isLeft != -1 && iAccept == 0) {
outputFile_ << myId_ << std::endl;
} else if ( isLeft != -1 && iAccept == 1) {
outputFile_ << ptId_ << std::endl;
}
stepCount_++;
return (iAccept == 1 ? true : false);
}