--- branches/development/src/parallel/ForceMatrixDecomposition.cpp 2011/08/12 19:59:56 1612 +++ branches/development/src/parallel/ForceMatrixDecomposition.cpp 2012/01/06 19:03:05 1668 @@ -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" @@ -229,30 +230,11 @@ namespace OpenMD { 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); } } } +#else excludesForAtom.clear(); excludesForAtom.resize(nLocal_); toposForAtom.clear(); @@ -285,7 +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(); } @@ -683,8 +685,9 @@ namespace OpenMD { } AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); - for (int i = 0; i < ns; i++) + for (int i = 0; i < ns; i++) snap_->atomData.skippedCharge[i] += skch_tmp[i]; + } nLocal_ = snap_->getNumberOfAtoms(); @@ -714,6 +717,13 @@ namespace OpenMD { 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 } @@ -826,22 +836,27 @@ 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]; - - // this situation should only arise in MPI simulations +#else + unique_id_1 = AtomLocalToGlobal[atom1]; + unique_id_2 = AtomLocalToGlobal[atom2]; +#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; + if ((unique_id_1 + unique_id_2) % 2 == 1) return true; } #endif + return false; } @@ -855,18 +870,13 @@ 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; @@ -991,8 +1001,8 @@ 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); @@ -1185,17 +1195,24 @@ namespace OpenMD { } } #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) ); @@ -1214,7 +1231,7 @@ 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 ); @@ -1222,18 +1239,20 @@ 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 }