/*
* Build the PairList, i.e., populate it with atom pairs.
*/
void PairList::build(CellList& cellList, bool reverseUpdateFlag)
{
// Precondition
assert(isAllocated());
Cell::NeighborArray neighbors;
double dRSq, cutoffSq;
const Cell* cellPtr;
Atom* atom1Ptr;
Atom* atom2Ptr;
Mask* maskPtr;
Vector dr;
int na; // number of atoms in this cell
int nn; // number of neighbors for a cell
int atom2Id; // atom Id for second atom
int i, j;
bool foundNeighbor;
// Set maximum squared-separation for pairs in Pairlist
cutoffSq = cutoff_*cutoff_;
// Initialize counters for primary atoms and neighbors
atom1Ptrs_.clear();
atom2Ptrs_.clear();
first_.clear();
first_.append(0);
// Find all neighbors (cell list)
cellPtr = cellList.begin();
while (cellPtr) {
cellPtr->getNeighbors(neighbors, reverseUpdateFlag);
na = cellPtr->nAtom();
nn = neighbors.size();
// Loop over primary atoms (atom1) in primary cell
for (i = 0; i < na; ++i) {
atom1Ptr = neighbors[i];
maskPtr = &(atom1Ptr->mask());
foundNeighbor = false;
// Loop over secondary atoms (atom2) in primary cell
for (j = 0; j < na; ++j) {
atom2Ptr = neighbors[j];
if (atom2Ptr > atom1Ptr) {
atom2Id = atom2Ptr->id();
if (!maskPtr->isMasked(atom2Id)) {
dr.subtract(atom2Ptr->position(), atom1Ptr->position());
dRSq = dr.square();
if (dRSq < cutoffSq) {
// If first neighbor of atom1, add atom1 to atom1Ptrs_
if (!foundNeighbor) {
atom1Ptrs_.append(atom1Ptr);
foundNeighbor = true;
}
// Append 2nd atom to atom2Ptrs_[]
atom2Ptrs_.append(atom2Ptr);
}
}
}
}
// Atoms in neighboring cells
for (j = na; j < nn; ++j) {
atom2Ptr = neighbors[j];
atom2Id = atom2Ptr->id();
if (!maskPtr->isMasked(atom2Id)) {
dr.subtract(atom2Ptr->position(), atom1Ptr->position());
dRSq = dr.square();
if (dRSq < cutoffSq) {
// If first_ neighbor, record iAtomId in atom1Ptrs_
if (!foundNeighbor) {
atom1Ptrs_.append(atom1Ptr);
foundNeighbor = true;
}
// Append Id of 2nd atom in pair to atom2Ptrs_[]
atom2Ptrs_.append(atom2Ptr);
}
}
}
// When finished with atom1, set next element of first_ array.
if (foundNeighbor) {
first_.append(atom2Ptrs_.size());
}
}
// Advance to next cell in a linked list
cellPtr = cellPtr->nextCellPtr();
}
// Postconditions
if (atom1Ptrs_.size()) {
if (first_.size() != atom1Ptrs_.size() + 1) {
UTIL_THROW("Array size problem");
}
if (first_[0] != 0) {
UTIL_THROW("Incorrect first element of first_");
}
if (first_[atom1Ptrs_.size()] != atom2Ptrs_.size()) {
UTIL_THROW("Incorrect last element of first_");
}
}
// Increment buildCounter_= number of times the list has been built.
++buildCounter_;
// Increment maxima
if (atom1Ptrs_.size() > maxNAtomLocal_) {
maxNAtomLocal_ = atom1Ptrs_.size();
}
if (atom2Ptrs_.size() > maxNPairLocal_) {
maxNPairLocal_ = atom2Ptrs_.size();
}
}
/*
* Evaluate change in energy, add Boltzmann factor to accumulator.
*/
void McMuExchange::sample(long iStep)
{
if (isAtInterval(iStep)) {
// Preconditions
if (!system().energyEnsemble().isIsothermal()) {
UTIL_THROW("EnergyEnsemble is not isothermal");
}
if (nMolecule_ != system().nMolecule(speciesId_)) {
UTIL_THROW("nMolecule has changed since setup");
}
McPairPotential& potential = system().pairPotential();
const CellList& cellList = potential.cellList();
System::MoleculeIterator molIter;
Atom* ptr0 = 0; // Pointer to first atom in molecule
Atom* ptr1 = 0; // Pointer to flipped atom
Atom* ptr2 = 0; // Pointer to neighboring atom
Mask* maskPtr = 0; // Mask of flipped atom
double rsq, dE, beta, boltzmann;
int j, k, nNeighbor, nFlip;
int i1, i2, id1, id2, t1, t2, t1New, iMol;
beta = system().energyEnsemble().beta();
nFlip = flipAtomIds_.size();
// Loop over molecules in species
iMol = 0;
system().begin(speciesId_, molIter);
for ( ; molIter.notEnd(); ++molIter) {
dE = 0.0;
ptr0 = &molIter->atom(0);
// Loop over flipped atoms
for (j = 0; j < nFlip; ++j) {
i1 = flipAtomIds_[j];
t1New = newTypeIds_[i1];
ptr1 = &molIter->atom(i1);
id1 = ptr1->id();
t1 = ptr1->typeId();
maskPtr = &(ptr1->mask());
// Loop over neighboring atoms
cellList.getNeighbors(ptr1->position(), neighbors_);
nNeighbor = neighbors_.size();
for (k = 0; k < nNeighbor; ++k) {
ptr2 = neighbors_[k];
id2 = ptr2->id();
// Check if atoms are identical
if (id2 != id1) {
// Check if pair is masked
if (!maskPtr->isMasked(*ptr2)) {
rsq = boundary().distanceSq(ptr1->position(),
ptr2->position());
t2 = ptr2->typeId();
if (&(ptr1->molecule()) != &(ptr2->molecule())) {
// Intermolecular atom pair
dE -= potential.energy(rsq, t1, t2);
dE += potential.energy(rsq, t1New, t2);
} else {
// Intramolecular atom pair
if (id2 > id1) {
dE -= potential.energy(rsq, t1, t2);
i2 = (int)(ptr2 - ptr0);
t2 = newTypeIds_[i2];
dE += potential.energy(rsq, t1New, t2);
} else {
i2 = (int)(ptr2 - ptr0);
if (!isAtomFlipped_[i2]) {
dE -= potential.energy(rsq, t1, t2);
t2 = newTypeIds_[i2];
dE += potential.energy(rsq, t1New, t2);
}
}
}
}
}
} // end loop over neighbors
} // end loop over flipped atoms
boltzmann = exp(-beta*dE);
accumulators_[iMol].sample(boltzmann);
++iMol;
} // end loop over molecules
}
}
/*
* Build the PairList, i.e., populate it with atom pairs.
*/
void PairList::build(CellList& cellList, bool reverseUpdateFlag)
{
// Precondition
assert(isAllocated());
Cell::NeighborArray neighbors;
double cutoffSq;
const Cell* cellPtr;
CellAtom* atom1Ptr;
CellAtom* atom2Ptr;
Mask* maskPtr;
Vector dr;
int na; // number of atoms in this cell
int nn; // number of neighbors for a cell
int i, j;
bool hasNeighbor;
// Set maximum squared-separation for pairs in Pairlist
cutoffSq = cutoff_*cutoff_;
// Initialize counters for primary atoms and neighbors
atom1Ptrs_.clear();
atom2Ptrs_.clear();
first_.clear();
first_.append(0);
// Copy positions and ids into cell list
cellList.update();
// Find all neighbors (cell list)
cellPtr = cellList.begin();
while (cellPtr) {
na = cellPtr->nAtom(); // # of atoms in cell
if (na) {
cellPtr->getNeighbors(neighbors, reverseUpdateFlag);
nn = neighbors.size();
// Loop over primary atoms (atom1) in primary cell
for (i = 0; i < na; ++i) {
atom1Ptr = neighbors[i];
maskPtr = atom1Ptr->maskPtr();
// Loop over secondary atoms
hasNeighbor = false;
for (j = i + 1; j < nn; ++j) {
atom2Ptr = neighbors[j];
dr.subtract(atom2Ptr->position(), atom1Ptr->position());
if (dr.square() < cutoffSq && !maskPtr->isMasked(atom2Ptr->id())) {
atom2Ptrs_.append(atom2Ptr->ptr());
hasNeighbor = true;
}
}
// Complete processing of atom1.
if (hasNeighbor) {
atom1Ptrs_.append(atom1Ptr->ptr());
first_.append(atom2Ptrs_.size());
}
} // for ia
} // if (na)
// Advance to next cell in a linked list
cellPtr = cellPtr->nextCellPtr();
}
// Postconditions
if (atom1Ptrs_.size()) {
if (first_.size() != atom1Ptrs_.size() + 1) {
UTIL_THROW("Array size problem");
}
if (first_[0] != 0) {
UTIL_THROW("Incorrect first element of first_");
}
if (first_[atom1Ptrs_.size()] != atom2Ptrs_.size()) {
UTIL_THROW("Incorrect last element of first_");
}
}
// Increment buildCounter_= number of times the list has been built.
++buildCounter_;
// Increment maxima
if (atom1Ptrs_.size() > maxNAtomLocal_) {
maxNAtomLocal_ = atom1Ptrs_.size();
}
if (atom2Ptrs_.size() > maxNPairLocal_) {
maxNPairLocal_ = atom2Ptrs_.size();
}
}
