/*
* 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();
}
}
/*
* 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();
}
}