void getNeighbors(
NeighborList& neighbors,
const VoxelItem& referencePoint,
const vector<set<int> >& exclusions,
bool reportSymmetricPairs,
double maxDistance,
double minDistance) const
{
// Loop over neighboring voxels
// TODO use more clever selection of neighboring voxels
assert(maxDistance > 0);
assert(minDistance >= 0);
assert(voxelSizeX > 0);
assert(voxelSizeY > 0);
assert(voxelSizeZ > 0);
const AtomIndex atomI = referencePoint.second;
const RealVec& locationI = *referencePoint.first;
double maxDistanceSquared = maxDistance * maxDistance;
double minDistanceSquared = minDistance * minDistance;
int dIndexX = int(maxDistance / voxelSizeX) + 1; // How may voxels away do we have to look?
int dIndexY = int(maxDistance / voxelSizeY) + 1;
int dIndexZ = int(maxDistance / voxelSizeZ) + 1;
VoxelIndex centerVoxelIndex = getVoxelIndex(locationI);
int lastx = centerVoxelIndex.x+dIndexX;
int lasty = centerVoxelIndex.y+dIndexY;
int lastz = centerVoxelIndex.z+dIndexZ;
if (usePeriodic) {
lastx = min(lastx, centerVoxelIndex.x-dIndexX+nx-1);
lasty = min(lasty, centerVoxelIndex.y-dIndexY+ny-1);
lastz = min(lastz, centerVoxelIndex.z-dIndexZ+nz-1);
}
for (int x = centerVoxelIndex.x - dIndexX; x <= lastx; ++x)
{
for (int y = centerVoxelIndex.y - dIndexY; y <= lasty; ++y)
{
for (int z = centerVoxelIndex.z - dIndexZ; z <= lastz; ++z)
{
VoxelIndex voxelIndex(x, y, z);
if (usePeriodic) {
voxelIndex.x = (x+nx)%nx;
voxelIndex.y = (y+ny)%ny;
voxelIndex.z = (z+nz)%nz;
}
if (voxelMap.find(voxelIndex) == voxelMap.end()) continue; // no such voxel; skip
const Voxel& voxel = voxelMap.find(voxelIndex)->second;
for (Voxel::const_iterator itemIter = voxel.begin(); itemIter != voxel.end(); ++itemIter)
{
const AtomIndex atomJ = itemIter->second;
const RealVec& locationJ = *itemIter->first;
// Ignore self hits
if (atomI == atomJ) continue;
// Ignore exclusions.
if (exclusions[atomI].find(atomJ) != exclusions[atomI].end()) continue;
double dSquared = compPairDistanceSquared(locationI, locationJ, periodicBoxSize, usePeriodic);
if (dSquared > maxDistanceSquared) continue;
if (dSquared < minDistanceSquared) continue;
neighbors.push_back( AtomPair(atomI, atomJ) );
if (reportSymmetricPairs)
neighbors.push_back( AtomPair(atomJ, atomI) );
}
}
}
}
}
void getNeighbors(
ThreeNeighborList& neighbors,
const VoxelItem& referencePoint,
double maxDistance,
double minDistance) const
{
// Loop over neighboring voxels
// TODO use more clever selection of neighboring voxels
assert(maxDistance > 0);
assert(minDistance >= 0);
assert(voxelSizeX > 0);
assert(voxelSizeY > 0);
assert(voxelSizeZ > 0);
const AtomIndex atomI = referencePoint.second;
const RealVec& locationI = *referencePoint.first;
double maxDistanceSquared = maxDistance * maxDistance;
double minDistanceSquared = minDistance * minDistance;
int dIndexX = int(maxDistance / voxelSizeX) + 1; // How may voxels away do we have to look?
int dIndexY = int(maxDistance / voxelSizeY) + 1;
int dIndexZ = int(maxDistance / voxelSizeZ) + 1;
VoxelIndex centerVoxelIndex = getVoxelIndex(locationI);
int lastx = centerVoxelIndex.x+dIndexX;
int lasty = centerVoxelIndex.y+dIndexY;
int lastz = centerVoxelIndex.z+dIndexZ;
if (usePeriodic) {
lastx = min(lastx, centerVoxelIndex.x-dIndexX+nx-1);
lasty = min(lasty, centerVoxelIndex.y-dIndexY+ny-1);
lastz = min(lastz, centerVoxelIndex.z-dIndexZ+nz-1);
}
std::vector<AtomIndex> nearbyAtoms;
std::vector<const RealVec*> nearbyAtomsLocation;
// Loop through nearby Voxels and create vectors of nearby Atoms and their locations
for (int x = centerVoxelIndex.x - dIndexX; x <= lastx; ++x)
{
for (int y = centerVoxelIndex.y - dIndexY; y <= lasty; ++y)
{
for (int z = centerVoxelIndex.z - dIndexZ; z <= lastz; ++z)
{
VoxelIndex voxelIndex(x, y, z);
if (usePeriodic) {
voxelIndex.x = (x+nx)%nx;
voxelIndex.y = (y+ny)%ny;
voxelIndex.z = (z+nz)%nz;
}
if (voxelMap.find(voxelIndex) == voxelMap.end()) continue; // no such voxel; skip
const Voxel& voxel = voxelMap.find(voxelIndex)->second;
for (Voxel::const_iterator itemIter = voxel.begin(); itemIter != voxel.end(); ++itemIter)
{
const AtomIndex atomJ = itemIter->second;
const RealVec& locationJ = *itemIter->first;
// Ignore self hits
if (atomI == atomJ) continue;
double dSquared = compPairDistanceSquared(locationI, locationJ, periodicBoxSize, usePeriodic);
if (dSquared > maxDistanceSquared) continue;
if (dSquared < minDistanceSquared) continue;
nearbyAtoms.push_back( atomJ );
nearbyAtomsLocation.push_back( itemIter->first );
} // for atom indices
} // for z
} // for y
} // for x
if (nearbyAtoms.size() >= 2)
{
// Loop through each combination of the reference atom (atomI) with each pair of nearby atoms atomJ and atomQ
for (unsigned int atomJindex=0; atomJindex<(nearbyAtoms.size()-1); atomJindex++)
{
for (unsigned int atomQindex=atomJindex+1; atomQindex<nearbyAtoms.size(); atomQindex++)
{
// check only distance Q-J, we checked I-J and I-Q in the previous loop
double dSquared = compPairDistanceSquared(*nearbyAtomsLocation[atomJindex], *nearbyAtomsLocation[atomQindex], periodicBoxSize, usePeriodic);
if (dSquared > maxDistanceSquared) continue;
if (dSquared < minDistanceSquared) continue;
AtomTriplet triplet = {atomI, nearbyAtoms[atomJindex], nearbyAtoms[atomQindex]};
neighbors.push_back(triplet);
}
}
}
}
