--- branches/development/src/parallel/ForceMatrixDecomposition.cpp 2011/05/12 17:00:14 1562 +++ trunk/src/parallel/ForceMatrixDecomposition.cpp 2013/10/31 18:18:57 1939 @@ -35,126 +35,660 @@ * * [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). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [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" #include "nonbonded/NonBondedInteraction.hpp" #include "brains/SnapshotManager.hpp" +#include "brains/PairList.hpp" 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(); -#ifdef IS_MPI - int nLocal = snap_->getNumberOfAtoms(); - int nGroups = snap_->getNumberOfCutoffGroups(); + ff_ = info_->getForceField(); + nLocal_ = snap_->getNumberOfAtoms(); + + nGroups_ = info_->getNLocalCutoffGroups(); + // gather the information for atomtype IDs (atids): + idents = info_->getIdentArray(); + regions = info_->getRegions(); + 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(); - AtomCommIntRow = new Communicator(nLocal); - AtomCommRealRow = new Communicator(nLocal); - AtomCommVectorRow = new Communicator(nLocal); - AtomCommMatrixRow = new Communicator(nLocal); + if (needVelocities_) + snap_->cgData.setStorageLayout(DataStorage::dslPosition | + DataStorage::dslVelocity); + else + snap_->cgData.setStorageLayout(DataStorage::dslPosition); + +#ifdef IS_MPI + + 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); + 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_); - int nAtomsInRow = AtomCommIntRow->getSize(); - int nAtomsInCol = AtomCommIntColumn->getSize(); - int nGroupsInRow = cgCommIntRow->getSize(); - int 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.resize(nAtomsInRow_); atomRowData.setStorageLayout(storageLayout_); - atomColData.resize(nAtomsInCol); + atomColData.resize(nAtomsInCol_); atomColData.setStorageLayout(storageLayout_); - cgRowData.resize(nGroupsInRow); + cgRowData.resize(nGroupsInRow_); cgRowData.setStorageLayout(DataStorage::dslPosition); - cgColData.resize(nGroupsInCol); - cgColData.setStorageLayout(DataStorage::dslPosition); + cgColData.resize(nGroupsInCol_); + if (needVelocities_) + // we only need column velocities if we need them. + cgColData.setStorageLayout(DataStorage::dslPosition | + DataStorage::dslVelocity); + else + cgColData.setStorageLayout(DataStorage::dslPosition); + + identsRow.resize(nAtomsInRow_); + identsCol.resize(nAtomsInCol_); - vector > pot_row(N_INTERACTION_FAMILIES, - vector (nAtomsInRow, 0.0)); - vector > pot_col(N_INTERACTION_FAMILIES, - vector (nAtomsInCol, 0.0)); + AtomPlanIntRow->gather(idents, identsRow); + AtomPlanIntColumn->gather(idents, identsCol); - - vector pot_local(N_INTERACTION_FAMILIES, 0.0); + regionsRow.resize(nAtomsInRow_); + regionsCol.resize(nAtomsInCol_); - // gather the information for atomtype IDs (atids): - vector identsLocal = info_->getIdentArray(); - identsRow.reserve(nAtomsInRow); - identsCol.reserve(nAtomsInCol); + AtomPlanIntRow->gather(regions, regionsRow); + AtomPlanIntColumn->gather(regions, regionsCol); - AtomCommIntRow->gather(identsLocal, identsRow); - AtomCommIntColumn->gather(identsLocal, identsCol); - - AtomLocalToGlobal = info_->getGlobalAtomIndices(); - AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); - AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); - - cgLocalToGlobal = info_->getGlobalGroupIndices(); - cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); - cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); + // allocate memory for the parallel objects + atypesRow.resize(nAtomsInRow_); + atypesCol.resize(nAtomsInCol_); - // still need: - // topoDist - // exclude + for (int i = 0; i < nAtomsInRow_; i++) + atypesRow[i] = ff_->getAtomType(identsRow[i]); + for (int i = 0; i < nAtomsInCol_; i++) + atypesCol[i] = ff_->getAtomType(identsCol[i]); + + pot_row.resize(nAtomsInRow_); + pot_col.resize(nAtomsInCol_); + + expot_row.resize(nAtomsInRow_); + expot_col.resize(nAtomsInCol_); + + AtomRowToGlobal.resize(nAtomsInRow_); + AtomColToGlobal.resize(nAtomsInCol_); + AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); + AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); + + cgRowToGlobal.resize(nGroupsInRow_); + cgColToGlobal.resize(nGroupsInCol_); + cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); + cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); + + massFactorsRow.resize(nAtomsInRow_); + massFactorsCol.resize(nAtomsInCol_); + AtomPlanRealRow->gather(massFactors, massFactorsRow); + AtomPlanRealColumn->gather(massFactors, massFactorsCol); + + groupListRow_.clear(); + groupListRow_.resize(nGroupsInRow_); + for (int i = 0; i < nGroupsInRow_; i++) { + int gid = cgRowToGlobal[i]; + for (int j = 0; j < nAtomsInRow_; j++) { + int aid = AtomRowToGlobal[j]; + if (globalGroupMembership[aid] == gid) + groupListRow_[i].push_back(j); + } + } + + groupListCol_.clear(); + groupListCol_.resize(nGroupsInCol_); + for (int i = 0; i < nGroupsInCol_; i++) { + int gid = cgColToGlobal[i]; + for (int j = 0; j < nAtomsInCol_; j++) { + int aid = AtomColToGlobal[j]; + if (globalGroupMembership[aid] == gid) + groupListCol_[i].push_back(j); + } + } + + excludesForAtom.clear(); + excludesForAtom.resize(nAtomsInRow_); + toposForAtom.clear(); + toposForAtom.resize(nAtomsInRow_); + topoDist.clear(); + topoDist.resize(nAtomsInRow_); + for (int i = 0; i < nAtomsInRow_; i++) { + int iglob = AtomRowToGlobal[i]; + + for (int j = 0; j < nAtomsInCol_; j++) { + int jglob = AtomColToGlobal[j]; + + if (excludes->hasPair(iglob, jglob)) + excludesForAtom[i].push_back(j); + + if (oneTwo->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(1); + } else { + if (oneThree->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(2); + } else { + if (oneFour->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(3); + } + } + } + } + } + +#else + excludesForAtom.clear(); + excludesForAtom.resize(nLocal_); + toposForAtom.clear(); + toposForAtom.resize(nLocal_); + topoDist.clear(); + topoDist.resize(nLocal_); + + for (int i = 0; i < nLocal_; i++) { + int iglob = AtomLocalToGlobal[i]; + + for (int j = 0; j < nLocal_; j++) { + int jglob = AtomLocalToGlobal[j]; + + if (excludes->hasPair(iglob, jglob)) + excludesForAtom[i].push_back(j); + + if (oneTwo->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(1); + } else { + if (oneThree->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(2); + } else { + if (oneFour->hasPair(iglob, jglob)) { + toposForAtom[i].push_back(j); + topoDist[i].push_back(3); + } + } + } + } + } #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(); + + } + + void ForceMatrixDecomposition::createGtypeCutoffMap() { + + GrCut.clear(); + GrCutSq.clear(); + GrlistSq.clear(); + + RealType tol = 1e-6; + largestRcut_ = 0.0; + int atid; + set atypes = info_->getSimulatedAtomTypes(); + + map atypeCutoff; + + for (set::iterator at = atypes.begin(); + at != atypes.end(); ++at){ + atid = (*at)->getIdent(); + if (userChoseCutoff_) + atypeCutoff[atid] = userCutoff_; + 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 + vector groupCutoffRow(nGroupsInRow_, 0.0); + groupRowToGtype.resize(nGroupsInRow_); + for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) { + vector atomListRow = getAtomsInGroupRow(cg1); + for (vector::iterator ia = atomListRow.begin(); + ia != atomListRow.end(); ++ia) { + int atom1 = (*ia); + atid = identsRow[atom1]; + if (atypeCutoff[atid] > groupCutoffRow[cg1]) { + groupCutoffRow[cg1] = atypeCutoff[atid]; + } + } + + bool gTypeFound = false; + for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { + if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) { + groupRowToGtype[cg1] = gt; + gTypeFound = true; + } + } + if (!gTypeFound) { + gTypeCutoffs.push_back( groupCutoffRow[cg1] ); + groupRowToGtype[cg1] = gTypeCutoffs.size() - 1; + } + + } + vector groupCutoffCol(nGroupsInCol_, 0.0); + groupColToGtype.resize(nGroupsInCol_); + for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) { + vector atomListCol = getAtomsInGroupColumn(cg2); + for (vector::iterator jb = atomListCol.begin(); + jb != atomListCol.end(); ++jb) { + int atom2 = (*jb); + atid = identsCol[atom2]; + if (atypeCutoff[atid] > groupCutoffCol[cg2]) { + groupCutoffCol[cg2] = atypeCutoff[atid]; + } + } + bool gTypeFound = false; + for (int gt = 0; gt < gTypeCutoffs.size(); gt++) { + if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) { + groupColToGtype[cg2] = gt; + gTypeFound = true; + } + } + if (!gTypeFound) { + gTypeCutoffs.push_back( groupCutoffCol[cg2] ); + groupColToGtype[cg2] = gTypeCutoffs.size() - 1; + } + } +#else + + vector groupCutoff(nGroups_, 0.0); + groupToGtype.resize(nGroups_); + for (int cg1 = 0; cg1 < nGroups_; cg1++) { + groupCutoff[cg1] = 0.0; + vector atomList = getAtomsInGroupRow(cg1); + for (vector::iterator ia = atomList.begin(); + ia != atomList.end(); ++ia) { + int atom1 = (*ia); + atid = idents[atom1]; + if (atypeCutoff[atid] > groupCutoff[cg1]) + groupCutoff[cg1] = atypeCutoff[atid]; + } + + bool gTypeFound = false; + for (unsigned int gt = 0; gt < gTypeCutoffs.size(); gt++) { + if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) { + groupToGtype[cg1] = gt; + gTypeFound = true; + } + } + if (!gTypeFound) { + gTypeCutoffs.push_back( groupCutoff[cg1] ); + groupToGtype[cg1] = gTypeCutoffs.size() - 1; + } + } +#endif + + // Now we find the maximum group cutoff value present in the simulation + + RealType groupMax = *max_element(gTypeCutoffs.begin(), + gTypeCutoffs.end()); + +#ifdef IS_MPI + MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, + MPI::MAX); +#endif + + RealType tradRcut = groupMax; + + GrCut.resize( gTypeCutoffs.size() ); + GrCutSq.resize( gTypeCutoffs.size() ); + GrlistSq.resize( gTypeCutoffs.size() ); + + + for (unsigned int i = 0; i < gTypeCutoffs.size(); i++) { + GrCut[i].resize( gTypeCutoffs.size() , 0.0); + GrCutSq[i].resize( gTypeCutoffs.size(), 0.0 ); + GrlistSq[i].resize( gTypeCutoffs.size(), 0.0 ); + + for (unsigned int j = 0; j < gTypeCutoffs.size(); j++) { + RealType thisRcut; + switch(cutoffPolicy_) { + case TRADITIONAL: + thisRcut = tradRcut; + break; + case MIX: + thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]); + break; + case MAX: + thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]); + break; + default: + sprintf(painCave.errMsg, + "ForceMatrixDecomposition::createGtypeCutoffMap " + "hit an unknown cutoff policy!\n"); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + break; + } + + GrCut[i][j] = thisRcut; + if (thisRcut > largestRcut_) largestRcut_ = thisRcut; + GrCutSq[i][j] = thisRcut * thisRcut; + GrlistSq[i][j] = pow(thisRcut + skinThickness_, 2); + + // pair key = make_pair(i,j); + // gTypeCutoffMap[key].first = thisRcut; + // gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); + // sanity check + + if (userChoseCutoff_) { + if (abs(GrCut[i][j] - userCutoff_) > 0.0001) { + sprintf(painCave.errMsg, + "ForceMatrixDecomposition::createGtypeCutoffMap " + "user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_); + painCave.severity = OPENMD_ERROR; + painCave.isFatal = 1; + simError(); + } + } + } + } } + + void ForceMatrixDecomposition::getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) { + int i, j; +#ifdef IS_MPI + i = groupRowToGtype[cg1]; + j = groupColToGtype[cg2]; +#else + i = groupToGtype[cg1]; + j = groupToGtype[cg2]; +#endif + rcut = GrCut[i][j]; + rcutsq = GrCutSq[i][j]; + rlistsq = GrlistSq[i][j]; + return; + //return gTypeCutoffMap[make_pair(i,j)]; + } + + int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) { + for (unsigned int j = 0; j < toposForAtom[atom1].size(); j++) { + if (toposForAtom[atom1][j] == atom2) + return topoDist[atom1][j]; + } + return 0; + } + + void ForceMatrixDecomposition::zeroWorkArrays() { + pairwisePot = 0.0; + embeddingPot = 0.0; + excludedPot = 0.0; + excludedSelfPot = 0.0; + +#ifdef IS_MPI + if (storageLayout_ & DataStorage::dslForce) { + fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero); + fill(atomColData.force.begin(), atomColData.force.end(), V3Zero); + } + + if (storageLayout_ & DataStorage::dslTorque) { + fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero); + fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero); + } + fill(pot_row.begin(), pot_row.end(), + Vector (0.0)); + fill(pot_col.begin(), pot_col.end(), + Vector (0.0)); + fill(expot_row.begin(), expot_row.end(), + Vector (0.0)); + + fill(expot_col.begin(), expot_col.end(), + Vector (0.0)); + + if (storageLayout_ & DataStorage::dslParticlePot) { + fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), + 0.0); + fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), + 0.0); + } + + if (storageLayout_ & DataStorage::dslDensity) { + fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0); + fill(atomColData.density.begin(), atomColData.density.end(), 0.0); + } + + if (storageLayout_ & DataStorage::dslFunctional) { + fill(atomRowData.functional.begin(), atomRowData.functional.end(), + 0.0); + fill(atomColData.functional.begin(), atomColData.functional.end(), + 0.0); + } + + if (storageLayout_ & DataStorage::dslFunctionalDerivative) { + fill(atomRowData.functionalDerivative.begin(), + 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); + } + + if (storageLayout_ & DataStorage::dslFlucQForce) { + fill(atomRowData.flucQFrc.begin(), + atomRowData.flucQFrc.end(), 0.0); + fill(atomColData.flucQFrc.begin(), + atomColData.flucQFrc.end(), 0.0); + } + + if (storageLayout_ & DataStorage::dslElectricField) { + fill(atomRowData.electricField.begin(), + atomRowData.electricField.end(), V3Zero); + fill(atomColData.electricField.begin(), + atomColData.electricField.end(), V3Zero); + } + +#endif + // even in parallel, we need to zero out the local arrays: + + if (storageLayout_ & DataStorage::dslParticlePot) { + fill(snap_->atomData.particlePot.begin(), + snap_->atomData.particlePot.end(), 0.0); + } + + if (storageLayout_ & DataStorage::dslDensity) { + 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); + } + } + + void ForceMatrixDecomposition::distributeData() { snap_ = sman_->getCurrentSnapshot(); storageLayout_ = sman_->getStorageLayout(); #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 (needVelocities_) { + // gather up the atomic velocities + AtomPlanVectorColumn->gather(snap_->atomData.velocity, + atomColData.velocity); + + cgPlanVectorColumn->gather(snap_->cgData.velocity, + cgColData.velocity); + } + // 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, - atomRowData.electroFrame); - AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, - atomColData.electroFrame); + + // if needed, gather the atomic eletrostatic information + if (storageLayout_ & DataStorage::dslDipole) { + AtomPlanVectorRow->gather(snap_->atomData.dipole, + atomRowData.dipole); + AtomPlanVectorColumn->gather(snap_->atomData.dipole, + atomColData.dipole); } + + if (storageLayout_ & DataStorage::dslQuadrupole) { + AtomPlanMatrixRow->gather(snap_->atomData.quadrupole, + atomRowData.quadrupole); + AtomPlanMatrixColumn->gather(snap_->atomData.quadrupole, + atomColData.quadrupole); + } + + // 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 } + /* collects information obtained during the pre-pair loop onto local + * data structures. + */ void ForceMatrixDecomposition::collectIntermediateData() { snap_ = sman_->getCurrentSnapshot(); storageLayout_ = sman_->getStorageLayout(); @@ -162,33 +696,52 @@ namespace OpenMD { if (storageLayout_ & DataStorage::dslDensity) { - AtomCommRealRow->scatter(atomRowData.density, + AtomPlanRealRow->scatter(atomRowData.density, snap_->atomData.density); int n = snap_->atomData.density.size(); - std::vector rho_tmp(n, 0.0); - AtomCommRealColumn->scatter(atomColData.density, rho_tmp); + vector rho_tmp(n, 0.0); + AtomPlanRealColumn->scatter(atomColData.density, rho_tmp); for (int i = 0; i < n; i++) snap_->atomData.density[i] += rho_tmp[i]; } + + // this isn't necessary if we don't have polarizable atoms, but + // we'll leave it here for now. + 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 } - + + /* + * redistributes information obtained during the pre-pair loop out to + * row and column-indexed data structures + */ void ForceMatrixDecomposition::distributeIntermediateData() { snap_ = sman_->getCurrentSnapshot(); 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 @@ -202,47 +755,243 @@ 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.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++) { + 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); - for (int i = 0; i < n; i++) + AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp); + for (int i = 0; i < nt; i++) snap_->atomData.torque[i] += trq_tmp[i]; } - - int nLocal = snap_->getNumberOfAtoms(); - vector > pot_temp(N_INTERACTION_FAMILIES, - vector (nLocal, 0.0)); + if (storageLayout_ & DataStorage::dslSkippedCharge) { + + int ns = snap_->atomData.skippedCharge.size(); + vector skch_tmp(ns, 0.0); + + 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; + } + + AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); + for (int i = 0; i < ns; i++) + snap_->atomData.skippedCharge[i] += skch_tmp[i]; + + } - for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { - AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); - for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { - pot_local[i] += pot_temp[i][ii]; + 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]; + } + + if (storageLayout_ & DataStorage::dslElectricField) { + + int nef = snap_->atomData.electricField.size(); + vector efield_tmp(nef, V3Zero); + + AtomPlanVectorRow->scatter(atomRowData.electricField, efield_tmp); + for (int i = 0; i < nef; i++) { + snap_->atomData.electricField[i] += efield_tmp[i]; + efield_tmp[i] = 0.0; + } + + AtomPlanVectorColumn->scatter(atomColData.electricField, efield_tmp); + for (int i = 0; i < nef; i++) + snap_->atomData.electricField[i] += efield_tmp[i]; + } + + + nLocal_ = snap_->getNumberOfAtoms(); + + vector pot_temp(nLocal_, + Vector (0.0)); + vector expot_temp(nLocal_, + Vector (0.0)); + + // scatter/gather pot_row into the members of my column + + AtomPlanPotRow->scatter(pot_row, pot_temp); + AtomPlanPotRow->scatter(expot_row, expot_temp); + + for (int ii = 0; ii < pot_temp.size(); ii++ ) + pairwisePot += pot_temp[ii]; + + for (int ii = 0; ii < expot_temp.size(); ii++ ) + excludedPot += expot_temp[ii]; + + if (storageLayout_ & DataStorage::dslParticlePot) { + // This is the pairwise contribution to the particle pot. The + // embedding contribution is added in each of the low level + // non-bonded routines. In single processor, this is done in + // unpackInteractionData, not in collectData. + for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { + for (int i = 0; i < nLocal_; i++) { + // factor of two is because the total potential terms are divided + // by 2 in parallel due to row/ column scatter + snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii); + } + } + } + + fill(pot_temp.begin(), pot_temp.end(), + Vector (0.0)); + fill(expot_temp.begin(), expot_temp.end(), + Vector (0.0)); + + AtomPlanPotColumn->scatter(pot_col, pot_temp); + AtomPlanPotColumn->scatter(expot_col, expot_temp); + + for (int ii = 0; ii < pot_temp.size(); ii++ ) + pairwisePot += pot_temp[ii]; + + for (int ii = 0; ii < expot_temp.size(); ii++ ) + excludedPot += expot_temp[ii]; + + if (storageLayout_ & DataStorage::dslParticlePot) { + // This is the pairwise contribution to the particle pot. The + // embedding contribution is added in each of the low level + // non-bonded routines. In single processor, this is done in + // unpackInteractionData, not in collectData. + for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { + for (int i = 0; i < nLocal_; i++) { + // factor of two is because the total potential terms are divided + // by 2 in parallel due to row/ column scatter + snap_->atomData.particlePot[i] += 2.0 * pot_temp[i](ii); + } + } + } + + if (storageLayout_ & DataStorage::dslParticlePot) { + int npp = snap_->atomData.particlePot.size(); + vector ppot_temp(npp, 0.0); + + // This is the direct or embedding contribution to the particle + // pot. + + AtomPlanRealRow->scatter(atomRowData.particlePot, ppot_temp); + for (int i = 0; i < npp; i++) { + snap_->atomData.particlePot[i] += ppot_temp[i]; + } + + fill(ppot_temp.begin(), ppot_temp.end(), 0.0); + + AtomPlanRealColumn->scatter(atomColData.particlePot, ppot_temp); + for (int i = 0; i < npp; i++) { + snap_->atomData.particlePot[i] += ppot_temp[i]; + } + } + + 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 = excludedPot[ii]; + RealType ploc2 = 0.0; + MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); + excludedPot[ii] = ploc2; + } + + // Here be dragons. + MPI::Intracomm col = colComm.getComm(); + + col.Allreduce(MPI::IN_PLACE, + &snap_->frameData.conductiveHeatFlux[0], 3, + MPI::REALTYPE, MPI::SUM); + + #endif + } + /** + * Collects information obtained during the post-pair (and embedding + * functional) loops onto local data structures. + */ + void ForceMatrixDecomposition::collectSelfData() { + snap_ = sman_->getCurrentSnapshot(); + storageLayout_ = sman_->getStorageLayout(); + +#ifdef IS_MPI + 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; + } + for (int ii = 0; ii < N_INTERACTION_FAMILIES; ii++) { + RealType ploc1 = excludedSelfPot[ii]; + RealType ploc2 = 0.0; + MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); + excludedSelfPot[ii] = ploc2; + } +#endif + + } + + + + int& ForceMatrixDecomposition::getNAtomsInRow() { +#ifdef IS_MPI + return nAtomsInRow_; +#else + return nLocal_; +#endif + } + + /** + * returns the list of atoms belonging to this group. + */ + vector& ForceMatrixDecomposition::getAtomsInGroupRow(int cg1){ +#ifdef IS_MPI + return groupListRow_[cg1]; +#else + return groupList_[cg1]; +#endif + } + + vector& ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2){ +#ifdef IS_MPI + return groupListCol_[cg2]; +#else + return groupList_[cg2]; +#endif + } Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ Vector3d d; @@ -253,11 +1002,29 @@ namespace OpenMD { d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; #endif - snap_->wrapVector(d); + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(d); + } return d; } + Vector3d& ForceMatrixDecomposition::getGroupVelocityColumn(int cg2){ +#ifdef IS_MPI + return cgColData.velocity[cg2]; +#else + return snap_->cgData.velocity[cg2]; +#endif + } + Vector3d& ForceMatrixDecomposition::getAtomVelocityColumn(int atom2){ +#ifdef IS_MPI + return atomColData.velocity[atom2]; +#else + return snap_->atomData.velocity[atom2]; +#endif + } + + Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){ Vector3d d; @@ -267,8 +1034,9 @@ namespace OpenMD { #else d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; #endif - - snap_->wrapVector(d); + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(d); + } return d; } @@ -280,10 +1048,28 @@ namespace OpenMD { #else d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; #endif - - snap_->wrapVector(d); + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(d); + } return d; } + + RealType& ForceMatrixDecomposition::getMassFactorRow(int atom1) { +#ifdef IS_MPI + return massFactorsRow[atom1]; +#else + return massFactors[atom1]; +#endif + } + + RealType& ForceMatrixDecomposition::getMassFactorColumn(int atom2) { +#ifdef IS_MPI + return massFactorsCol[atom2]; +#else + return massFactors[atom2]; +#endif + + } Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ Vector3d d; @@ -293,11 +1079,79 @@ namespace OpenMD { #else d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; #endif - - snap_->wrapVector(d); + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(d); + } return d; } + vector& ForceMatrixDecomposition::getExcludesForAtom(int atom1) { + return excludesForAtom[atom1]; + } + + /** + * We need to exclude some overcounted interactions that result from + * the parallel decomposition. + */ + bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2, int cg1, int cg2) { + 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]; + // group1 = cgRowToGlobal[cg1]; + // group2 = cgColToGlobal[cg2]; +#else + unique_id_1 = AtomLocalToGlobal[atom1]; + unique_id_2 = AtomLocalToGlobal[atom2]; + int group1 = cgLocalToGlobal[cg1]; + int group2 = cgLocalToGlobal[cg2]; +#endif + + 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; + } +#endif + +#ifndef IS_MPI + if (group1 == group2) { + if (unique_id_1 < unique_id_2) 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) { + + // 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) == atom2 ) return true; + } + + return false; + } + + void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ #ifdef IS_MPI atomRowData.force[atom1] += fg; @@ -312,181 +1166,464 @@ namespace OpenMD { #else snap_->atomData.force[atom2] += fg; #endif - } // filling interaction blocks with pointers - InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { + void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, + int atom1, int atom2) { - InteractionData idat; + idat.excluded = excludeAtomPair(atom1, atom2); + #ifdef IS_MPI + //idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); + idat.atid1 = identsRow[atom1]; + idat.atid2 = identsCol[atom2]; + + if (regionsRow[atom1] >= 0 && regionsCol[atom2] >= 0) { + idat.sameRegion = (regionsRow[atom1] == regionsCol[atom2]); + } else { + idat.sameRegion = false; + } + if (storageLayout_ & DataStorage::dslAmat) { idat.A1 = &(atomRowData.aMat[atom1]); idat.A2 = &(atomColData.aMat[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::dslDipole) { + idat.dipole1 = &(atomRowData.dipole[atom1]); + idat.dipole2 = &(atomColData.dipole[atom2]); + } + + if (storageLayout_ & DataStorage::dslQuadrupole) { + idat.quadrupole1 = &(atomRowData.quadrupole[atom1]); + idat.quadrupole2 = &(atomColData.quadrupole[atom2]); + } + if (storageLayout_ & DataStorage::dslDensity) { idat.rho1 = &(atomRowData.density[atom1]); idat.rho2 = &(atomColData.density[atom2]); } + if (storageLayout_ & DataStorage::dslFunctional) { + idat.frho1 = &(atomRowData.functional[atom1]); + idat.frho2 = &(atomColData.functional[atom2]); + } + if (storageLayout_ & DataStorage::dslFunctionalDerivative) { idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); } + + if (storageLayout_ & DataStorage::dslParticlePot) { + idat.particlePot1 = &(atomRowData.particlePot[atom1]); + idat.particlePot2 = &(atomColData.particlePot[atom2]); + } + + if (storageLayout_ & DataStorage::dslSkippedCharge) { + idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); + idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); + } + + if (storageLayout_ & DataStorage::dslFlucQPosition) { + idat.flucQ1 = &(atomRowData.flucQPos[atom1]); + idat.flucQ2 = &(atomColData.flucQPos[atom2]); + } + #else + + //idat.atypes = make_pair( atypesLocal[atom1], atypesLocal[atom2]); + idat.atid1 = idents[atom1]; + idat.atid2 = idents[atom2]; + + if (regions[atom1] >= 0 && regions[atom2] >= 0) { + idat.sameRegion = (regions[atom1] == regions[atom2]); + } else { + idat.sameRegion = false; + } + if (storageLayout_ & DataStorage::dslAmat) { idat.A1 = &(snap_->atomData.aMat[atom1]); idat.A2 = &(snap_->atomData.aMat[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::dslDensity) { + if (storageLayout_ & DataStorage::dslDipole) { + idat.dipole1 = &(snap_->atomData.dipole[atom1]); + idat.dipole2 = &(snap_->atomData.dipole[atom2]); + } + + if (storageLayout_ & DataStorage::dslQuadrupole) { + idat.quadrupole1 = &(snap_->atomData.quadrupole[atom1]); + idat.quadrupole2 = &(snap_->atomData.quadrupole[atom2]); + } + + if (storageLayout_ & DataStorage::dslDensity) { idat.rho1 = &(snap_->atomData.density[atom1]); idat.rho2 = &(snap_->atomData.density[atom2]); } + if (storageLayout_ & DataStorage::dslFunctional) { + idat.frho1 = &(snap_->atomData.functional[atom1]); + idat.frho2 = &(snap_->atomData.functional[atom2]); + } + if (storageLayout_ & DataStorage::dslFunctionalDerivative) { idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); } + + if (storageLayout_ & DataStorage::dslParticlePot) { + idat.particlePot1 = &(snap_->atomData.particlePot[atom1]); + idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); + } + + if (storageLayout_ & DataStorage::dslSkippedCharge) { + idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); + idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); + } + + if (storageLayout_ & DataStorage::dslFlucQPosition) { + idat.flucQ1 = &(snap_->atomData.flucQPos[atom1]); + idat.flucQ2 = &(snap_->atomData.flucQPos[atom2]); + } + #endif - } - InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ - InteractionData idat; - skippedCharge1 - skippedCharge2 - rij - d - electroMult - sw - f -#ifdef IS_MPI - if (storageLayout_ & DataStorage::dslElectroFrame) { - idat.eFrame1 = &(atomRowData.electroFrame[atom1]); - idat.eFrame2 = &(atomColData.electroFrame[atom2]); + + void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { +#ifdef IS_MPI + pot_row[atom1] += RealType(0.5) * *(idat.pot); + pot_col[atom2] += RealType(0.5) * *(idat.pot); + expot_row[atom1] += RealType(0.5) * *(idat.excludedPot); + expot_col[atom2] += RealType(0.5) * *(idat.excludedPot); + + atomRowData.force[atom1] += *(idat.f1); + atomColData.force[atom2] -= *(idat.f1); + + if (storageLayout_ & DataStorage::dslFlucQForce) { + atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1); + atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2); } - if (storageLayout_ & DataStorage::dslTorque) { - idat.t1 = &(atomRowData.torque[atom1]); - idat.t2 = &(atomColData.torque[atom2]); + + if (storageLayout_ & DataStorage::dslElectricField) { + atomRowData.electricField[atom1] += *(idat.eField1); + atomColData.electricField[atom2] += *(idat.eField2); } +#else + pairwisePot += *(idat.pot); + excludedPot += *(idat.excludedPot); + + snap_->atomData.force[atom1] += *(idat.f1); + snap_->atomData.force[atom2] -= *(idat.f1); + + if (idat.doParticlePot) { + // This is the pairwise contribution to the particle pot. The + // embedding contribution is added in each of the low level + // non-bonded routines. In parallel, this calculation is done + // in collectData, not in unpackInteractionData. + snap_->atomData.particlePot[atom1] += *(idat.vpair) * *(idat.sw); + snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw); + } - } - SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { - } + if (storageLayout_ & DataStorage::dslFlucQForce) { + snap_->atomData.flucQFrc[atom1] -= *(idat.dVdFQ1); + snap_->atomData.flucQFrc[atom2] -= *(idat.dVdFQ2); + } + if (storageLayout_ & DataStorage::dslElectricField) { + snap_->atomData.electricField[atom1] += *(idat.eField1); + snap_->atomData.electricField[atom2] += *(idat.eField2); + } +#endif + + } + /* * buildNeighborList * * first element of pair is row-indexed CutoffGroup * second element of pair is column-indexed CutoffGroup */ - vector > buildNeighborList() { - Vector3d dr, invWid, rs, shift; - Vector3i cc, m1v, m2s; - RealType rrNebr; - int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset; + void ForceMatrixDecomposition::buildNeighborList(vector >& neighborList) { + + neighborList.clear(); + groupCutoffs cuts; + bool doAllPairs = false; + RealType rList_ = (largestRcut_ + skinThickness_); + RealType rcut, rcutsq, rlistsq; + Snapshot* snap_ = sman_->getCurrentSnapshot(); + Mat3x3d box; + Mat3x3d invBox; - vector > neighborList; - Vector3i nCells; - Vector3d invWid, r; + Vector3d rs, scaled, dr; + Vector3i whichCell; + int cellIndex; - rList_ = (rCut_ + skinThickness_); - rl2 = rList_ * rList_; - - snap_ = sman_->getCurrentSnapshot(); - Mat3x3d Hmat = snap_->getHmat(); - Vector3d Hx = Hmat.getColumn(0); - Vector3d Hy = Hmat.getColumn(1); - Vector3d Hz = Hmat.getColumn(2); - - nCells.x() = (int) ( Hx.length() )/ rList_; - nCells.y() = (int) ( Hy.length() )/ rList_; - nCells.z() = (int) ( Hz.length() )/ rList_; - - for (i = 0; i < nGroupsInRow; i++) { - rs = cgRowData.position[i]; - snap_->scaleVector(rs); +#ifdef IS_MPI + cellListRow_.clear(); + cellListCol_.clear(); +#else + cellList_.clear(); +#endif + + if (!usePeriodicBoundaryConditions_) { + box = snap_->getBoundingBox(); + invBox = snap_->getInvBoundingBox(); + } else { + box = snap_->getHmat(); + invBox = snap_->getInvHmat(); } + Vector3d boxX = box.getColumn(0); + Vector3d boxY = box.getColumn(1); + Vector3d boxZ = box.getColumn(2); + + nCells_.x() = int( boxX.length() / rList_ ); + nCells_.y() = int( boxY.length() / rList_ ); + nCells_.z() = int( boxZ.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; + + int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); + +#ifdef IS_MPI + cellListRow_.resize(nCtot); + cellListCol_.resize(nCtot); +#else + 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 = invBox * 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; + // Handle the special case when an object is exactly on the + // boundary (a scaled coordinate of 1.0 is the same as + // scaled coordinate of 0.0) + if (scaled[j] >= 1.0) scaled[j] -= 1.0; + } + + // 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 = invBox * 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; + // Handle the special case when an object is exactly on the + // boundary (a scaled coordinate of 1.0 is the same as + // scaled coordinate of 0.0) + if (scaled[j] >= 1.0) scaled[j] -= 1.0; + } + + // 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 = invBox * 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; + // Handle the special case when an object is exactly on the + // boundary (a scaled coordinate of 1.0 is the same as + // scaled coordinate of 0.0) + if (scaled[j] >= 1.0) scaled[j] -= 1.0; + } + + // find xyz-indices of cell that cutoffGroup is in. + whichCell.x() = int(nCells_.x() * scaled.x()); + whichCell.y() = int(nCells_.y() * scaled.y()); + whichCell.z() = int(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); + } - VDiv (invWid, cells, region); - for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1; - for (n = 0; n < nMol; n ++) { - VSAdd (rs, mol[n].r, 0.5, region); - VMul (cc, rs, invWid); - c = VLinear (cc, cells) + nMol; - cellList[n] = cellList[c]; - cellList[c] = n; - } - nebrTabLen = 0; - for (m1z = 0; m1z < cells.z(); m1z++) { - for (m1y = 0; m1y < cells.y(); m1y++) { - for (m1x = 0; m1x < cells.x(); m1x++) { - Vector3i m1v(m1x, m1y, m1z); - m1 = VLinear(m1v, cells) + nMol; - for (offset = 0; offset < nOffset_; offset++) { - m2v = m1v + cellOffsets_[offset]; - shift = V3Zero(); +#endif - if (m2v.x() >= cells.x) { - m2v.x() = 0; - shift.x() = region.x(); - } else if (m2v.x() < 0) { - m2v.x() = cells.x() - 1; - shift.x() = - region.x(); - } + 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) { + + Vector3i m2v = m1v + (*os); + - if (m2v.y() >= cells.y()) { - m2v.y() = 0; - shift.y() = region.y(); - } else if (m2v.y() < 0) { - m2v.y() = cells.y() - 1; - shift.y() = - region.y(); - } + 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; + } - m2 = VLinear (m2v, cells) + nMol; - for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) { - for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) { - if (m1 != m2 || j2 < j1) { - dr = mol[j1].r - mol[j2].r; - VSub (dr, mol[j1].r, mol[j2].r); - VVSub (dr, shift); - if (VLenSq (dr) < rrNebr) { - neighborList.push_back(make_pair(j1, j2)); + 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) { + + // 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)]; + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(dr); } + getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq ); + if (dr.lengthSquare() < rlistsq) { + 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 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)]; + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(dr); + } + getGroupCutoffs( (*j1), (*j2), rcut, rcutsq, rlistsq ); + if (dr.lengthSquare() < rlistsq) { + 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]; + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(dr); + } + getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq); + if (dr.lengthSquare() < rlistsq) { + neighborList.push_back(make_pair(j1, j2)); + } + } + } +#else + // 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]; + if (usePeriodicBoundaryConditions_) { + snap_->wrapVector(dr); + } + getGroupCutoffs( j1, j2, rcut, rcutsq, rlistsq ); + if (dr.lengthSquare() < rlistsq) { + 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]); } - - } //end namespace OpenMD