--- branches/development/src/parallel/ForceMatrixDecomposition.cpp 2011/07/12 20:33:14 1592 +++ branches/development/src/parallel/ForceMatrixDecomposition.cpp 2012/05/19 14:21:02 1713 @@ -36,7 +36,8 @@ * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include "parallel/ForceMatrixDecomposition.hpp" #include "math/SquareMatrix3.hpp" @@ -47,11 +48,48 @@ namespace OpenMD { using namespace std; namespace OpenMD { + ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) { + + // In a parallel computation, row and colum scans must visit all + // surrounding cells (not just the 14 upper triangular blocks that + // are used when the processor can see all pairs) +#ifdef IS_MPI + cellOffsets_.clear(); + cellOffsets_.push_back( Vector3i(-1,-1,-1) ); + cellOffsets_.push_back( Vector3i( 0,-1,-1) ); + cellOffsets_.push_back( Vector3i( 1,-1,-1) ); + cellOffsets_.push_back( Vector3i(-1, 0,-1) ); + cellOffsets_.push_back( Vector3i( 0, 0,-1) ); + cellOffsets_.push_back( Vector3i( 1, 0,-1) ); + cellOffsets_.push_back( Vector3i(-1, 1,-1) ); + cellOffsets_.push_back( Vector3i( 0, 1,-1) ); + cellOffsets_.push_back( Vector3i( 1, 1,-1) ); + cellOffsets_.push_back( Vector3i(-1,-1, 0) ); + cellOffsets_.push_back( Vector3i( 0,-1, 0) ); + cellOffsets_.push_back( Vector3i( 1,-1, 0) ); + cellOffsets_.push_back( Vector3i(-1, 0, 0) ); + cellOffsets_.push_back( Vector3i( 0, 0, 0) ); + cellOffsets_.push_back( Vector3i( 1, 0, 0) ); + cellOffsets_.push_back( Vector3i(-1, 1, 0) ); + cellOffsets_.push_back( Vector3i( 0, 1, 0) ); + cellOffsets_.push_back( Vector3i( 1, 1, 0) ); + cellOffsets_.push_back( Vector3i(-1,-1, 1) ); + cellOffsets_.push_back( Vector3i( 0,-1, 1) ); + cellOffsets_.push_back( Vector3i( 1,-1, 1) ); + cellOffsets_.push_back( Vector3i(-1, 0, 1) ); + cellOffsets_.push_back( Vector3i( 0, 0, 1) ); + cellOffsets_.push_back( Vector3i( 1, 0, 1) ); + cellOffsets_.push_back( Vector3i(-1, 1, 1) ); + cellOffsets_.push_back( Vector3i( 0, 1, 1) ); + cellOffsets_.push_back( Vector3i( 1, 1, 1) ); +#endif + } + + /** * distributeInitialData is essentially a copy of the older fortran * SimulationSetup */ - void ForceMatrixDecomposition::distributeInitialData() { snap_ = sman_->getCurrentSnapshot(); storageLayout_ = sman_->getStorageLayout(); @@ -74,28 +112,31 @@ namespace OpenMD { #ifdef IS_MPI - AtomCommIntRow = new Communicator(nLocal_); - AtomCommRealRow = new Communicator(nLocal_); - AtomCommVectorRow = new Communicator(nLocal_); - AtomCommMatrixRow = new Communicator(nLocal_); - AtomCommPotRow = new Communicator(nLocal_); + MPI::Intracomm row = rowComm.getComm(); + MPI::Intracomm col = colComm.getComm(); - AtomCommIntColumn = new Communicator(nLocal_); - AtomCommRealColumn = new Communicator(nLocal_); - AtomCommVectorColumn = new Communicator(nLocal_); - AtomCommMatrixColumn = new Communicator(nLocal_); - AtomCommPotColumn = new Communicator(nLocal_); + AtomPlanIntRow = new Plan(row, nLocal_); + AtomPlanRealRow = new Plan(row, nLocal_); + AtomPlanVectorRow = new Plan(row, nLocal_); + AtomPlanMatrixRow = new Plan(row, nLocal_); + AtomPlanPotRow = new Plan(row, nLocal_); - cgCommIntRow = new Communicator(nGroups_); - cgCommVectorRow = new Communicator(nGroups_); - cgCommIntColumn = new Communicator(nGroups_); - cgCommVectorColumn = new Communicator(nGroups_); + AtomPlanIntColumn = new Plan(col, nLocal_); + AtomPlanRealColumn = new Plan(col, nLocal_); + AtomPlanVectorColumn = new Plan(col, nLocal_); + AtomPlanMatrixColumn = new Plan(col, nLocal_); + AtomPlanPotColumn = new Plan(col, nLocal_); - nAtomsInRow_ = AtomCommIntRow->getSize(); - nAtomsInCol_ = AtomCommIntColumn->getSize(); - nGroupsInRow_ = cgCommIntRow->getSize(); - nGroupsInCol_ = cgCommIntColumn->getSize(); + cgPlanIntRow = new Plan(row, nGroups_); + cgPlanVectorRow = new Plan(row, nGroups_); + cgPlanIntColumn = new Plan(col, nGroups_); + cgPlanVectorColumn = new Plan(col, nGroups_); + nAtomsInRow_ = AtomPlanIntRow->getSize(); + nAtomsInCol_ = AtomPlanIntColumn->getSize(); + nGroupsInRow_ = cgPlanIntRow->getSize(); + nGroupsInCol_ = cgPlanIntColumn->getSize(); + // Modify the data storage objects with the correct layouts and sizes: atomRowData.resize(nAtomsInRow_); atomRowData.setStorageLayout(storageLayout_); @@ -109,8 +150,8 @@ namespace OpenMD { identsRow.resize(nAtomsInRow_); identsCol.resize(nAtomsInCol_); - AtomCommIntRow->gather(idents, identsRow); - AtomCommIntColumn->gather(idents, identsCol); + AtomPlanIntRow->gather(idents, identsRow); + AtomPlanIntColumn->gather(idents, identsCol); // allocate memory for the parallel objects atypesRow.resize(nAtomsInRow_); @@ -126,18 +167,18 @@ namespace OpenMD { AtomRowToGlobal.resize(nAtomsInRow_); AtomColToGlobal.resize(nAtomsInCol_); - AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); - AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); - + AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); + AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); + cgRowToGlobal.resize(nGroupsInRow_); cgColToGlobal.resize(nGroupsInCol_); - cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); - cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); + cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); + cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); massFactorsRow.resize(nAtomsInRow_); massFactorsCol.resize(nAtomsInCol_); - AtomCommRealRow->gather(massFactors, massFactorsRow); - AtomCommRealColumn->gather(massFactors, massFactorsCol); + AtomPlanRealRow->gather(massFactors, massFactorsRow); + AtomPlanRealColumn->gather(massFactors, massFactorsCol); groupListRow_.clear(); groupListRow_.resize(nGroupsInRow_); @@ -193,26 +234,7 @@ namespace OpenMD { } } -#endif - - // allocate memory for the parallel objects - atypesLocal.resize(nLocal_); - - for (int i = 0; i < nLocal_; i++) - atypesLocal[i] = ff_->getAtomType(idents[i]); - - groupList_.clear(); - groupList_.resize(nGroups_); - for (int i = 0; i < nGroups_; i++) { - int gid = cgLocalToGlobal[i]; - for (int j = 0; j < nLocal_; j++) { - int aid = AtomLocalToGlobal[j]; - if (globalGroupMembership[aid] == gid) { - groupList_[i].push_back(j); - } - } - } - +#else excludesForAtom.clear(); excludesForAtom.resize(nLocal_); toposForAtom.clear(); @@ -245,7 +267,27 @@ namespace OpenMD { } } } - +#endif + + // allocate memory for the parallel objects + atypesLocal.resize(nLocal_); + + for (int i = 0; i < nLocal_; i++) + atypesLocal[i] = ff_->getAtomType(idents[i]); + + groupList_.clear(); + groupList_.resize(nGroups_); + for (int i = 0; i < nGroups_; i++) { + int gid = cgLocalToGlobal[i]; + for (int j = 0; j < nLocal_; j++) { + int aid = AtomLocalToGlobal[j]; + if (globalGroupMembership[aid] == gid) { + groupList_[i].push_back(j); + } + } + } + + createGtypeCutoffMap(); } @@ -483,6 +525,19 @@ namespace OpenMD { atomColData.skippedCharge.end(), 0.0); } + if (storageLayout_ & DataStorage::dslElectricField) { + fill(atomRowData.electricField.begin(), + atomRowData.electricField.end(), V3Zero); + fill(atomColData.electricField.begin(), + atomColData.electricField.end(), V3Zero); + } + if (storageLayout_ & DataStorage::dslFlucQForce) { + fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(), + 0.0); + fill(atomColData.flucQFrc.begin(), atomColData.flucQFrc.end(), + 0.0); + } + #endif // even in parallel, we need to zero out the local arrays: @@ -495,19 +550,26 @@ namespace OpenMD { fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0); } + if (storageLayout_ & DataStorage::dslFunctional) { fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0); } + if (storageLayout_ & DataStorage::dslFunctionalDerivative) { 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); } - + + if (storageLayout_ & DataStorage::dslElectricField) { + fill(snap_->atomData.electricField.begin(), + snap_->atomData.electricField.end(), V3Zero); + } } @@ -517,33 +579,44 @@ namespace OpenMD { #ifdef IS_MPI // gather up the atomic positions - AtomCommVectorRow->gather(snap_->atomData.position, + AtomPlanVectorRow->gather(snap_->atomData.position, atomRowData.position); - AtomCommVectorColumn->gather(snap_->atomData.position, + AtomPlanVectorColumn->gather(snap_->atomData.position, atomColData.position); // gather up the cutoff group positions - cgCommVectorRow->gather(snap_->cgData.position, + + cgPlanVectorRow->gather(snap_->cgData.position, cgRowData.position); - cgCommVectorColumn->gather(snap_->cgData.position, + + cgPlanVectorColumn->gather(snap_->cgData.position, cgColData.position); + // if needed, gather the atomic rotation matrices if (storageLayout_ & DataStorage::dslAmat) { - AtomCommMatrixRow->gather(snap_->atomData.aMat, + AtomPlanMatrixRow->gather(snap_->atomData.aMat, atomRowData.aMat); - AtomCommMatrixColumn->gather(snap_->atomData.aMat, + AtomPlanMatrixColumn->gather(snap_->atomData.aMat, atomColData.aMat); } // if needed, gather the atomic eletrostatic frames if (storageLayout_ & DataStorage::dslElectroFrame) { - AtomCommMatrixRow->gather(snap_->atomData.electroFrame, + AtomPlanMatrixRow->gather(snap_->atomData.electroFrame, atomRowData.electroFrame); - AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, + AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame, atomColData.electroFrame); } + // if needed, gather the atomic fluctuating charge values + if (storageLayout_ & DataStorage::dslFlucQPosition) { + AtomPlanRealRow->gather(snap_->atomData.flucQPos, + atomRowData.flucQPos); + AtomPlanRealColumn->gather(snap_->atomData.flucQPos, + atomColData.flucQPos); + } + #endif } @@ -557,15 +630,27 @@ namespace OpenMD { if (storageLayout_ & DataStorage::dslDensity) { - AtomCommRealRow->scatter(atomRowData.density, + AtomPlanRealRow->scatter(atomRowData.density, snap_->atomData.density); int n = snap_->atomData.density.size(); vector rho_tmp(n, 0.0); - AtomCommRealColumn->scatter(atomColData.density, rho_tmp); + AtomPlanRealColumn->scatter(atomColData.density, rho_tmp); for (int i = 0; i < n; i++) snap_->atomData.density[i] += rho_tmp[i]; } + + if (storageLayout_ & DataStorage::dslElectricField) { + + AtomPlanVectorRow->scatter(atomRowData.electricField, + snap_->atomData.electricField); + + int n = snap_->atomData.electricField.size(); + vector field_tmp(n, V3Zero); + AtomPlanVectorColumn->scatter(atomColData.electricField, field_tmp); + for (int i = 0; i < n; i++) + snap_->atomData.electricField[i] += field_tmp[i]; + } #endif } @@ -578,16 +663,16 @@ namespace OpenMD { storageLayout_ = sman_->getStorageLayout(); #ifdef IS_MPI if (storageLayout_ & DataStorage::dslFunctional) { - AtomCommRealRow->gather(snap_->atomData.functional, + AtomPlanRealRow->gather(snap_->atomData.functional, atomRowData.functional); - AtomCommRealColumn->gather(snap_->atomData.functional, + AtomPlanRealColumn->gather(snap_->atomData.functional, atomColData.functional); } if (storageLayout_ & DataStorage::dslFunctionalDerivative) { - AtomCommRealRow->gather(snap_->atomData.functionalDerivative, + AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, atomRowData.functionalDerivative); - AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, + AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, atomColData.functionalDerivative); } #endif @@ -601,28 +686,29 @@ namespace OpenMD { int n = snap_->atomData.force.size(); vector frc_tmp(n, V3Zero); - AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); + AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp); for (int i = 0; i < n; i++) { snap_->atomData.force[i] += frc_tmp[i]; frc_tmp[i] = 0.0; } - AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); - for (int i = 0; i < n; i++) + AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp); + for (int i = 0; i < n; i++) { snap_->atomData.force[i] += frc_tmp[i]; + } if (storageLayout_ & DataStorage::dslTorque) { int nt = snap_->atomData.torque.size(); vector trq_tmp(nt, V3Zero); - AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); + AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp); 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); + AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp); for (int i = 0; i < nt; i++) snap_->atomData.torque[i] += trq_tmp[i]; } @@ -632,17 +718,35 @@ namespace OpenMD { int ns = snap_->atomData.skippedCharge.size(); vector skch_tmp(ns, 0.0); - AtomCommRealRow->scatter(atomRowData.skippedCharge, skch_tmp); + AtomPlanRealRow->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++) + AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); + for (int i = 0; i < ns; i++) snap_->atomData.skippedCharge[i] += skch_tmp[i]; + } + if (storageLayout_ & DataStorage::dslFlucQForce) { + + int nq = snap_->atomData.flucQFrc.size(); + vector fqfrc_tmp(nq, 0.0); + + AtomPlanRealRow->scatter(atomRowData.flucQFrc, fqfrc_tmp); + for (int i = 0; i < nq; i++) { + snap_->atomData.flucQFrc[i] += fqfrc_tmp[i]; + fqfrc_tmp[i] = 0.0; + } + + AtomPlanRealColumn->scatter(atomColData.flucQFrc, fqfrc_tmp); + for (int i = 0; i < nq; i++) + snap_->atomData.flucQFrc[i] += fqfrc_tmp[i]; + + } + nLocal_ = snap_->getNumberOfAtoms(); vector pot_temp(nLocal_, @@ -650,7 +754,7 @@ namespace OpenMD { // scatter/gather pot_row into the members of my column - AtomCommPotRow->scatter(pot_row, pot_temp); + AtomPlanPotRow->scatter(pot_row, pot_temp); for (int ii = 0; ii < pot_temp.size(); ii++ ) pairwisePot += pot_temp[ii]; @@ -658,10 +762,25 @@ namespace OpenMD { fill(pot_temp.begin(), pot_temp.end(), Vector (0.0)); - AtomCommPotColumn->scatter(pot_col, pot_temp); + AtomPlanPotColumn->scatter(pot_col, pot_temp); for (int ii = 0; ii < pot_temp.size(); ii++ ) pairwisePot += pot_temp[ii]; + + for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { + RealType ploc1 = pairwisePot[ii]; + RealType ploc2 = 0.0; + MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); + pairwisePot[ii] = ploc2; + } + + for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { + RealType ploc1 = embeddingPot[ii]; + RealType ploc2 = 0.0; + MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); + embeddingPot[ii] = ploc2; + } + #endif } @@ -774,22 +893,27 @@ namespace OpenMD { */ bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { int unique_id_1, unique_id_2; - + #ifdef IS_MPI // in MPI, we have to look up the unique IDs for each atom unique_id_1 = AtomRowToGlobal[atom1]; unique_id_2 = AtomColToGlobal[atom2]; +#else + unique_id_1 = AtomLocalToGlobal[atom1]; + unique_id_2 = AtomLocalToGlobal[atom2]; +#endif - // this situation should only arise in MPI simulations if (unique_id_1 == unique_id_2) return true; - + +#ifdef IS_MPI // this prevents us from doing the pair on multiple processors if (unique_id_1 < unique_id_2) { if ((unique_id_1 + unique_id_2) % 2 == 0) return true; } else { - if ((unique_id_1 + unique_id_2) % 2 == 1) return true; + if ((unique_id_1 + unique_id_2) % 2 == 1) return true; } #endif + return false; } @@ -803,19 +927,13 @@ namespace OpenMD { * 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_2 = atom2; -#endif + + // excludesForAtom was constructed to use row/column indices in the MPI + // version, and to use local IDs in the non-MPI version: for (vector::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i) { - if ( (*i) == unique_id_2 ) return true; + if ( (*i) == atom2 ) return true; } return false; @@ -890,7 +1008,12 @@ namespace OpenMD { } #else + + // cerr << "atoms = " << atom1 << " " << atom2 << "\n"; + // cerr << "pos1 = " << snap_->atomData.position[atom1] << "\n"; + // cerr << "pos2 = " << snap_->atomData.position[atom2] << "\n"; + idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); //idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), // ff_->getAtomType(idents[atom2]) ); @@ -940,16 +1063,24 @@ namespace OpenMD { void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { #ifdef IS_MPI - pot_row[atom1] += 0.5 * *(idat.pot); - pot_col[atom2] += 0.5 * *(idat.pot); + pot_row[atom1] += RealType(0.5) * *(idat.pot); + pot_col[atom2] += RealType(0.5) * *(idat.pot); atomRowData.force[atom1] += *(idat.f1); atomColData.force[atom2] -= *(idat.f1); + + // should particle pot be done here also? #else pairwisePot += *(idat.pot); snap_->atomData.force[atom1] += *(idat.f1); snap_->atomData.force[atom2] -= *(idat.f1); + + if (idat.doParticlePot) { + snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw); + snap_->atomData.particlePot[atom2] -= *(idat.vpair) * *(idat.sw); + } + #endif } @@ -1031,7 +1162,6 @@ namespace OpenMD { // 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]; @@ -1056,6 +1186,7 @@ namespace OpenMD { // 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]; @@ -1076,11 +1207,12 @@ namespace OpenMD { whichCell.z() = nCells_.z() * scaled.z(); // find single index of this cell: - cellIndex = Vlinear(whichCell, nCells_); + 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++) { @@ -1093,7 +1225,8 @@ namespace OpenMD { os != cellOffsets_.end(); ++os) { Vector3i m2v = m1v + (*os); - + + if (m2v.x() >= nCells_.x()) { m2v.x() = 0; } else if (m2v.x() < 0) { @@ -1111,7 +1244,7 @@ namespace OpenMD { } else if (m2v.z() < 0) { m2v.z() = nCells_.z() - 1; } - + int m2 = Vlinear (m2v, nCells_); #ifdef IS_MPI @@ -1120,32 +1253,36 @@ namespace OpenMD { 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))); - } - } + // In parallel, we need to visit *all* pairs of row + // & column indicies and will divide labor in the + // force evaluation later. + 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)) { + // we're in the same cell and the global index of + // the j2 cutoff group is greater than or equal to + // the j1 cutoff group. Note that Rappaport's code + // has a "less than" conditional here, but that + // deals with atom-by-atom computation. OpenMD + // allows atoms within a single cutoff group to + // interact with each other. + + + + if (m2 != m1 || (*j2) >= (*j1) ) { + dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; snap_->wrapVector(dr); cuts = getGroupCutoffs( (*j1), (*j2) ); @@ -1164,7 +1301,7 @@ namespace OpenMD { // branch to do all cutoff group pairs #ifdef IS_MPI for (int j1 = 0; j1 < nGroupsInRow_; j1++) { - for (int j2 = 0; j2 < nGroupsInCol_; j2++) { + for (int j2 = 0; j2 < nGroupsInCol_; j2++) { dr = cgColData.position[j2] - cgRowData.position[j1]; snap_->wrapVector(dr); cuts = getGroupCutoffs( j1, j2 ); @@ -1172,18 +1309,20 @@ namespace OpenMD { neighborList.push_back(make_pair(j1, j2)); } } - } + } #else - for (int j1 = 0; j1 < nGroups_ - 1; j1++) { - for (int j2 = j1 + 1; j2 < nGroups_; j2++) { + // include all groups here. + for (int j1 = 0; j1 < nGroups_; j1++) { + // include self group interactions j2 == j1 + for (int j2 = j1; 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 }