--- branches/development/src/parallel/ForceMatrixDecomposition.cpp 2011/06/17 20:16:35 1584 +++ branches/development/src/parallel/ForceMatrixDecomposition.cpp 2011/07/10 16:05:34 1589 @@ -57,20 +57,20 @@ namespace OpenMD { storageLayout_ = sman_->getStorageLayout(); ff_ = info_->getForceField(); nLocal_ = snap_->getNumberOfAtoms(); - + nGroups_ = info_->getNLocalCutoffGroups(); - cerr << "in dId, nGroups = " << nGroups_ << "\n"; // gather the information for atomtype IDs (atids): idents = info_->getIdentArray(); AtomLocalToGlobal = info_->getGlobalAtomIndices(); cgLocalToGlobal = info_->getGlobalGroupIndices(); vector globalGroupMembership = info_->getGlobalGroupMembership(); + massFactors = info_->getMassFactors(); - PairList excludes = info_->getExcludedInteractions(); - PairList oneTwo = info_->getOneTwoInteractions(); - PairList oneThree = info_->getOneThreeInteractions(); - PairList oneFour = info_->getOneFourInteractions(); + PairList* excludes = info_->getExcludedInteractions(); + PairList* oneTwo = info_->getOneTwoInteractions(); + PairList* oneThree = info_->getOneThreeInteractions(); + PairList* oneFour = info_->getOneFourInteractions(); #ifdef IS_MPI @@ -112,6 +112,16 @@ namespace OpenMD { AtomCommIntRow->gather(idents, identsRow); AtomCommIntColumn->gather(idents, identsCol); + // allocate memory for the parallel objects + AtomRowToGlobal.resize(nAtomsInRow_); + AtomColToGlobal.resize(nAtomsInCol_); + cgRowToGlobal.resize(nGroupsInRow_); + cgColToGlobal.resize(nGroupsInCol_); + massFactorsRow.resize(nAtomsInRow_); + massFactorsCol.resize(nAtomsInCol_); + pot_row.resize(nAtomsInRow_); + pot_col.resize(nAtomsInCol_); + AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); @@ -143,8 +153,8 @@ namespace OpenMD { } } - skipsForAtom.clear(); - skipsForAtom.resize(nAtomsInRow_); + excludesForAtom.clear(); + excludesForAtom.resize(nAtomsInRow_); toposForAtom.clear(); toposForAtom.resize(nAtomsInRow_); topoDist.clear(); @@ -155,18 +165,18 @@ namespace OpenMD { for (int j = 0; j < nAtomsInCol_; j++) { int jglob = AtomColToGlobal[j]; - if (excludes.hasPair(iglob, jglob)) - skipsForAtom[i].push_back(j); + if (excludes->hasPair(iglob, jglob)) + excludesForAtom[i].push_back(j); - if (oneTwo.hasPair(iglob, jglob)) { + if (oneTwo->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(1); } else { - if (oneThree.hasPair(iglob, jglob)) { + if (oneThree->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(2); } else { - if (oneFour.hasPair(iglob, jglob)) { + if (oneFour->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(3); } @@ -189,8 +199,8 @@ namespace OpenMD { } } - skipsForAtom.clear(); - skipsForAtom.resize(nLocal_); + excludesForAtom.clear(); + excludesForAtom.resize(nLocal_); toposForAtom.clear(); toposForAtom.resize(nLocal_); topoDist.clear(); @@ -202,18 +212,18 @@ namespace OpenMD { for (int j = 0; j < nLocal_; j++) { int jglob = AtomLocalToGlobal[j]; - if (excludes.hasPair(iglob, jglob)) - skipsForAtom[i].push_back(j); + if (excludes->hasPair(iglob, jglob)) + excludesForAtom[i].push_back(j); - if (oneTwo.hasPair(iglob, jglob)) { + if (oneTwo->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(1); } else { - if (oneThree.hasPair(iglob, jglob)) { + if (oneThree->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(2); } else { - if (oneFour.hasPair(iglob, jglob)) { + if (oneFour->hasPair(iglob, jglob)) { toposForAtom[i].push_back(j); topoDist[i].push_back(3); } @@ -223,29 +233,27 @@ namespace OpenMD { } createGtypeCutoffMap(); + } void ForceMatrixDecomposition::createGtypeCutoffMap() { - + RealType tol = 1e-6; RealType rc; int atid; set atypes = info_->getSimulatedAtomTypes(); - vector atypeCutoff; - atypeCutoff.resize( atypes.size() ); + map atypeCutoff; for (set::iterator at = atypes.begin(); at != atypes.end(); ++at){ atid = (*at)->getIdent(); - - if (userChoseCutoff_) + if (userChoseCutoff_) atypeCutoff[atid] = userCutoff_; - else + else atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); } vector gTypeCutoffs; - // first we do a single loop over the cutoff groups to find the // largest cutoff for any atypes present in this group. #ifdef IS_MPI @@ -303,8 +311,6 @@ namespace OpenMD { vector groupCutoff(nGroups_, 0.0); groupToGtype.resize(nGroups_); - - cerr << "nGroups = " << nGroups_ << "\n"; for (int cg1 = 0; cg1 < nGroups_; cg1++) { groupCutoff[cg1] = 0.0; @@ -333,7 +339,6 @@ namespace OpenMD { } #endif - cerr << "gTypeCutoffs.size() = " << gTypeCutoffs.size() << "\n"; // Now we find the maximum group cutoff value present in the simulation RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); @@ -454,6 +459,13 @@ namespace OpenMD { atomRowData.functionalDerivative.end(), 0.0); fill(atomColData.functionalDerivative.begin(), atomColData.functionalDerivative.end(), 0.0); + } + + if (storageLayout_ & DataStorage::dslSkippedCharge) { + fill(atomRowData.skippedCharge.begin(), + atomRowData.skippedCharge.end(), 0.0); + fill(atomColData.skippedCharge.begin(), + atomColData.skippedCharge.end(), 0.0); } #else @@ -475,6 +487,10 @@ namespace OpenMD { fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0); } + if (storageLayout_ & DataStorage::dslSkippedCharge) { + fill(snap_->atomData.skippedCharge.begin(), + snap_->atomData.skippedCharge.end(), 0.0); + } #endif } @@ -582,19 +598,35 @@ namespace OpenMD { if (storageLayout_ & DataStorage::dslTorque) { - int nt = snap_->atomData.force.size(); + int nt = snap_->atomData.torque.size(); vector trq_tmp(nt, V3Zero); AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); - for (int i = 0; i < n; i++) { + for (int i = 0; i < nt; i++) { snap_->atomData.torque[i] += trq_tmp[i]; trq_tmp[i] = 0.0; } AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); - for (int i = 0; i < n; i++) + for (int i = 0; i < nt; i++) snap_->atomData.torque[i] += trq_tmp[i]; } + + if (storageLayout_ & DataStorage::dslSkippedCharge) { + + int ns = snap_->atomData.skippedCharge.size(); + vector skch_tmp(ns, 0.0); + + AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); + for (int i = 0; i < ns; i++) { + snap_->atomData.skippedCharge[i] = skch_tmp[i]; + skch_tmp[i] = 0.0; + } + + AtomCommRealColumn->scatter(atomColData.skippedCharge, skch_tmp); + for (int i = 0; i < ns; i++) + snap_->atomData.skippedCharge[i] += skch_tmp[i]; + } nLocal_ = snap_->getNumberOfAtoms(); @@ -691,7 +723,6 @@ namespace OpenMD { #ifdef IS_MPI return massFactorsRow[atom1]; #else - cerr << "mfs = " << massFactors.size() << " atom1 = " << atom1 << "\n"; return massFactors[atom1]; #endif } @@ -718,15 +749,12 @@ namespace OpenMD { return d; } - vector ForceMatrixDecomposition::getSkipsForAtom(int atom1) { - return skipsForAtom[atom1]; + vector ForceMatrixDecomposition::getExcludesForAtom(int atom1) { + return excludesForAtom[atom1]; } /** - * There are a number of reasons to skip a pair or a - * particle. Mostly we do this to exclude atoms who are involved in - * short range interactions (bonds, bends, torsions), but we also - * need to exclude some overcounted interactions that result from + * We need to exclude some overcounted interactions that result from * the parallel decomposition. */ bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { @@ -746,14 +774,32 @@ namespace OpenMD { } else { if ((unique_id_1 + unique_id_2) % 2 == 1) return true; } +#endif + return false; + } + + /** + * We need to handle the interactions for atoms who are involved in + * the same rigid body as well as some short range interactions + * (bonds, bends, torsions) differently from other interactions. + * We'll still visit the pairwise routines, but with a flag that + * tells those routines to exclude the pair from direct long range + * interactions. Some indirect interactions (notably reaction + * field) must still be handled for these pairs. + */ + bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { + int unique_id_2; + +#ifdef IS_MPI + // in MPI, we have to look up the unique IDs for the row atom. + unique_id_2 = AtomColToGlobal[atom2]; #else // in the normal loop, the atom numbers are unique - unique_id_1 = atom1; unique_id_2 = atom2; #endif - for (vector::iterator i = skipsForAtom[atom1].begin(); - i != skipsForAtom[atom1].end(); ++i) { + for (vector::iterator i = excludesForAtom[atom1].begin(); + i != excludesForAtom[atom1].end(); ++i) { if ( (*i) == unique_id_2 ) return true; } @@ -779,7 +825,10 @@ namespace OpenMD { // filling interaction blocks with pointers void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, - int atom1, int atom2) { + int atom1, int atom2) { + + idat.excluded = excludeAtomPair(atom1, atom2); + #ifdef IS_MPI idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), @@ -820,6 +869,11 @@ namespace OpenMD { idat.particlePot2 = &(atomColData.particlePot[atom2]); } + if (storageLayout_ & DataStorage::dslSkippedCharge) { + idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); + idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); + } + #else idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), @@ -860,6 +914,10 @@ namespace OpenMD { idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); } + if (storageLayout_ & DataStorage::dslSkippedCharge) { + idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); + idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); + } #endif } @@ -877,63 +935,9 @@ namespace OpenMD { snap_->atomData.force[atom1] += *(idat.f1); snap_->atomData.force[atom2] -= *(idat.f1); #endif - + } - - void ForceMatrixDecomposition::fillSkipData(InteractionData &idat, - int atom1, int atom2) { -#ifdef IS_MPI - idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), - ff_->getAtomType(identsCol[atom2]) ); - - if (storageLayout_ & DataStorage::dslElectroFrame) { - idat.eFrame1 = &(atomRowData.electroFrame[atom1]); - idat.eFrame2 = &(atomColData.electroFrame[atom2]); - } - - if (storageLayout_ & DataStorage::dslTorque) { - idat.t1 = &(atomRowData.torque[atom1]); - idat.t2 = &(atomColData.torque[atom2]); - } - - if (storageLayout_ & DataStorage::dslSkippedCharge) { - idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); - idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); - } -#else - idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), - ff_->getAtomType(idents[atom2]) ); - - if (storageLayout_ & DataStorage::dslElectroFrame) { - idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); - idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); - } - - if (storageLayout_ & DataStorage::dslTorque) { - idat.t1 = &(snap_->atomData.torque[atom1]); - idat.t2 = &(snap_->atomData.torque[atom2]); - } - - if (storageLayout_ & DataStorage::dslSkippedCharge) { - idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); - idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); - } -#endif - } - - - void ForceMatrixDecomposition::unpackSkipData(InteractionData &idat, int atom1, int atom2) { -#ifdef IS_MPI - pot_row[atom1] += 0.5 * *(idat.pot); - pot_col[atom2] += 0.5 * *(idat.pot); -#else - pairwisePot += *(idat.pot); -#endif - - } - - /* * buildNeighborList * @@ -944,6 +948,8 @@ namespace OpenMD { vector > neighborList; groupCutoffs cuts; + bool doAllPairs = false; + #ifdef IS_MPI cellListRow_.clear(); cellListCol_.clear(); @@ -963,6 +969,12 @@ namespace OpenMD { nCells_.y() = (int) ( Hy.length() )/ rList_; nCells_.z() = (int) ( Hz.length() )/ rList_; + // handle small boxes where the cell offsets can end up repeating cells + + if (nCells_.x() < 3) doAllPairs = true; + if (nCells_.y() < 3) doAllPairs = true; + if (nCells_.z() < 3) doAllPairs = true; + Mat3x3d invHmat = snap_->getInvHmat(); Vector3d rs, scaled, dr; Vector3i whichCell; @@ -976,167 +988,195 @@ namespace OpenMD { cellList_.resize(nCtot); #endif + if (!doAllPairs) { #ifdef IS_MPI - for (int i = 0; i < nGroupsInRow_; i++) { - rs = cgRowData.position[i]; - // scaled positions relative to the box vectors - scaled = invHmat * rs; - - // wrap the vector back into the unit box by subtracting integer box - // numbers - for (int j = 0; j < 3; j++) { - scaled[j] -= roundMe(scaled[j]); - scaled[j] += 0.5; - } - - // find xyz-indices of cell that cutoffGroup is in. - whichCell.x() = nCells_.x() * scaled.x(); - whichCell.y() = nCells_.y() * scaled.y(); - whichCell.z() = nCells_.z() * scaled.z(); - - // find single index of this cell: - cellIndex = Vlinear(whichCell, nCells_); - - // add this cutoff group to the list of groups in this cell; - cellListRow_[cellIndex].push_back(i); - } - - for (int i = 0; i < nGroupsInCol_; i++) { - rs = cgColData.position[i]; - - // scaled positions relative to the box vectors - scaled = invHmat * rs; - - // wrap the vector back into the unit box by subtracting integer box - // numbers - for (int j = 0; j < 3; j++) { - scaled[j] -= roundMe(scaled[j]); - scaled[j] += 0.5; + for (int i = 0; i < nGroupsInRow_; i++) { + rs = cgRowData.position[i]; + + // scaled positions relative to the box vectors + scaled = invHmat * rs; + + // wrap the vector back into the unit box by subtracting integer box + // numbers + for (int j = 0; j < 3; j++) { + scaled[j] -= roundMe(scaled[j]); + scaled[j] += 0.5; + } + + // find xyz-indices of cell that cutoffGroup is in. + whichCell.x() = nCells_.x() * scaled.x(); + whichCell.y() = nCells_.y() * scaled.y(); + whichCell.z() = nCells_.z() * scaled.z(); + + // find single index of this cell: + cellIndex = Vlinear(whichCell, nCells_); + + // add this cutoff group to the list of groups in this cell; + cellListRow_[cellIndex].push_back(i); } - - // find xyz-indices of cell that cutoffGroup is in. - whichCell.x() = nCells_.x() * scaled.x(); - whichCell.y() = nCells_.y() * scaled.y(); - whichCell.z() = nCells_.z() * scaled.z(); - - // find single index of this cell: - cellIndex = Vlinear(whichCell, nCells_); - - // add this cutoff group to the list of groups in this cell; - cellListCol_[cellIndex].push_back(i); - } + + for (int i = 0; i < nGroupsInCol_; i++) { + rs = cgColData.position[i]; + + // scaled positions relative to the box vectors + scaled = invHmat * rs; + + // wrap the vector back into the unit box by subtracting integer box + // numbers + for (int j = 0; j < 3; j++) { + scaled[j] -= roundMe(scaled[j]); + scaled[j] += 0.5; + } + + // find xyz-indices of cell that cutoffGroup is in. + whichCell.x() = nCells_.x() * scaled.x(); + whichCell.y() = nCells_.y() * scaled.y(); + whichCell.z() = nCells_.z() * scaled.z(); + + // find single index of this cell: + cellIndex = Vlinear(whichCell, nCells_); + + // add this cutoff group to the list of groups in this cell; + cellListCol_[cellIndex].push_back(i); + } #else - for (int i = 0; i < nGroups_; i++) { - rs = snap_->cgData.position[i]; - - // scaled positions relative to the box vectors - scaled = invHmat * rs; - - // wrap the vector back into the unit box by subtracting integer box - // numbers - for (int j = 0; j < 3; j++) { - scaled[j] -= roundMe(scaled[j]); - scaled[j] += 0.5; + for (int i = 0; i < nGroups_; i++) { + rs = snap_->cgData.position[i]; + + // scaled positions relative to the box vectors + scaled = invHmat * rs; + + // wrap the vector back into the unit box by subtracting integer box + // numbers + for (int j = 0; j < 3; j++) { + scaled[j] -= roundMe(scaled[j]); + scaled[j] += 0.5; + } + + // find xyz-indices of cell that cutoffGroup is in. + whichCell.x() = nCells_.x() * scaled.x(); + whichCell.y() = nCells_.y() * scaled.y(); + whichCell.z() = nCells_.z() * scaled.z(); + + // find single index of this cell: + cellIndex = Vlinear(whichCell, nCells_); + + // add this cutoff group to the list of groups in this cell; + cellList_[cellIndex].push_back(i); } - - // find xyz-indices of cell that cutoffGroup is in. - whichCell.x() = nCells_.x() * scaled.x(); - whichCell.y() = nCells_.y() * scaled.y(); - whichCell.z() = nCells_.z() * scaled.z(); - - // find single index of this cell: - cellIndex = Vlinear(whichCell, nCells_); - - // add this cutoff group to the list of groups in this cell; - cellList_[cellIndex].push_back(i); - } #endif - for (int m1z = 0; m1z < nCells_.z(); m1z++) { - for (int m1y = 0; m1y < nCells_.y(); m1y++) { - for (int m1x = 0; m1x < nCells_.x(); m1x++) { - Vector3i m1v(m1x, m1y, m1z); - int m1 = Vlinear(m1v, nCells_); - - for (vector::iterator os = cellOffsets_.begin(); - os != cellOffsets_.end(); ++os) { + for (int m1z = 0; m1z < nCells_.z(); m1z++) { + for (int m1y = 0; m1y < nCells_.y(); m1y++) { + for (int m1x = 0; m1x < nCells_.x(); m1x++) { + Vector3i m1v(m1x, m1y, m1z); + int m1 = Vlinear(m1v, nCells_); - Vector3i m2v = m1v + (*os); - - if (m2v.x() >= nCells_.x()) { - m2v.x() = 0; - } else if (m2v.x() < 0) { - m2v.x() = nCells_.x() - 1; - } - - if (m2v.y() >= nCells_.y()) { - m2v.y() = 0; - } else if (m2v.y() < 0) { - m2v.y() = nCells_.y() - 1; - } - - if (m2v.z() >= nCells_.z()) { - m2v.z() = 0; - } else if (m2v.z() < 0) { - m2v.z() = nCells_.z() - 1; - } - - int m2 = Vlinear (m2v, nCells_); - + for (vector::iterator os = cellOffsets_.begin(); + os != cellOffsets_.end(); ++os) { + + Vector3i m2v = m1v + (*os); + + if (m2v.x() >= nCells_.x()) { + m2v.x() = 0; + } else if (m2v.x() < 0) { + m2v.x() = nCells_.x() - 1; + } + + if (m2v.y() >= nCells_.y()) { + m2v.y() = 0; + } else if (m2v.y() < 0) { + m2v.y() = nCells_.y() - 1; + } + + if (m2v.z() >= nCells_.z()) { + m2v.z() = 0; + } else if (m2v.z() < 0) { + m2v.z() = nCells_.z() - 1; + } + + int m2 = Vlinear (m2v, nCells_); + #ifdef IS_MPI - for (vector::iterator j1 = cellListRow_[m1].begin(); - j1 != cellListRow_[m1].end(); ++j1) { - for (vector::iterator j2 = cellListCol_[m2].begin(); - j2 != cellListCol_[m2].end(); ++j2) { - - // Always do this if we're in different cells or if - // we're in the same cell and the global index of the - // j2 cutoff group is less than the j1 cutoff group - - if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { - dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; - snap_->wrapVector(dr); - cuts = getGroupCutoffs( (*j1), (*j2) ); - if (dr.lengthSquare() < cuts.third) { - neighborList.push_back(make_pair((*j1), (*j2))); + for (vector::iterator j1 = cellListRow_[m1].begin(); + j1 != cellListRow_[m1].end(); ++j1) { + for (vector::iterator j2 = cellListCol_[m2].begin(); + j2 != cellListCol_[m2].end(); ++j2) { + + // Always do this if we're in different cells or if + // we're in the same cell and the global index of the + // j2 cutoff group is less than the j1 cutoff group + + if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { + dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; + snap_->wrapVector(dr); + cuts = getGroupCutoffs( (*j1), (*j2) ); + if (dr.lengthSquare() < cuts.third) { + neighborList.push_back(make_pair((*j1), (*j2))); + } } } } - } #else - - for (vector::iterator j1 = cellList_[m1].begin(); - j1 != cellList_[m1].end(); ++j1) { - for (vector::iterator j2 = cellList_[m2].begin(); - j2 != cellList_[m2].end(); ++j2) { - - // Always do this if we're in different cells or if - // we're in the same cell and the global index of the - // j2 cutoff group is less than the j1 cutoff group - - if (m2 != m1 || (*j2) < (*j1)) { - dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; - snap_->wrapVector(dr); - cuts = getGroupCutoffs( (*j1), (*j2) ); - if (dr.lengthSquare() < cuts.third) { - neighborList.push_back(make_pair((*j1), (*j2))); + + for (vector::iterator j1 = cellList_[m1].begin(); + j1 != cellList_[m1].end(); ++j1) { + for (vector::iterator j2 = cellList_[m2].begin(); + j2 != cellList_[m2].end(); ++j2) { + + // Always do this if we're in different cells or if + // we're in the same cell and the global index of the + // j2 cutoff group is less than the j1 cutoff group + + if (m2 != m1 || (*j2) < (*j1)) { + dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; + snap_->wrapVector(dr); + cuts = getGroupCutoffs( (*j1), (*j2) ); + if (dr.lengthSquare() < cuts.third) { + neighborList.push_back(make_pair((*j1), (*j2))); + } } } } - } #endif + } } } } + } else { + // branch to do all cutoff group pairs +#ifdef IS_MPI + for (int j1 = 0; j1 < nGroupsInRow_; j1++) { + for (int j2 = 0; j2 < nGroupsInCol_; j2++) { + dr = cgColData.position[j2] - cgRowData.position[j1]; + snap_->wrapVector(dr); + cuts = getGroupCutoffs( j1, j2 ); + if (dr.lengthSquare() < cuts.third) { + neighborList.push_back(make_pair(j1, j2)); + } + } + } +#else + for (int j1 = 0; j1 < nGroups_ - 1; j1++) { + for (int j2 = j1 + 1; j2 < nGroups_; j2++) { + dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; + snap_->wrapVector(dr); + cuts = getGroupCutoffs( j1, j2 ); + if (dr.lengthSquare() < cuts.third) { + neighborList.push_back(make_pair(j1, j2)); + } + } + } +#endif } - + // save the local cutoff group positions for the check that is // done on each loop: saved_CG_positions_.clear(); for (int i = 0; i < nGroups_; i++) saved_CG_positions_.push_back(snap_->cgData.position[i]); - + return neighborList; } } //end namespace OpenMD