--- branches/development/src/parallel/ForceMatrixDecomposition.cpp 2012/05/19 14:21:02 1713 +++ branches/development/src/parallel/ForceMatrixDecomposition.cpp 2012/06/14 01:58:35 1755 @@ -95,7 +95,7 @@ namespace OpenMD { storageLayout_ = sman_->getStorageLayout(); ff_ = info_->getForceField(); nLocal_ = snap_->getNumberOfAtoms(); - + nGroups_ = info_->getNLocalCutoffGroups(); // gather the information for atomtype IDs (atids): idents = info_->getIdentArray(); @@ -109,7 +109,13 @@ namespace OpenMD { PairList* oneTwo = info_->getOneTwoInteractions(); PairList* oneThree = info_->getOneThreeInteractions(); PairList* oneFour = info_->getOneFourInteractions(); - + + if (needVelocities_) + snap_->cgData.setStorageLayout(DataStorage::dslPosition | + DataStorage::dslVelocity); + else + snap_->cgData.setStorageLayout(DataStorage::dslPosition); + #ifdef IS_MPI MPI::Intracomm row = rowComm.getComm(); @@ -145,8 +151,13 @@ namespace OpenMD { cgRowData.resize(nGroupsInRow_); cgRowData.setStorageLayout(DataStorage::dslPosition); cgColData.resize(nGroupsInCol_); - cgColData.setStorageLayout(DataStorage::dslPosition); - + 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_); @@ -523,6 +534,13 @@ namespace OpenMD { 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) { @@ -531,6 +549,7 @@ namespace OpenMD { fill(atomColData.electricField.begin(), atomColData.electricField.end(), V3Zero); } + if (storageLayout_ & DataStorage::dslFlucQForce) { fill(atomRowData.flucQFrc.begin(), atomRowData.flucQFrc.end(), 0.0); @@ -592,6 +611,17 @@ namespace OpenMD { 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) { @@ -758,7 +788,21 @@ namespace OpenMD { for (int ii = 0; ii < pot_temp.size(); ii++ ) pairwisePot += pot_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)); @@ -766,7 +810,41 @@ namespace OpenMD { for (int ii = 0; ii < pot_temp.size(); ii++ ) pairwisePot += pot_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; @@ -780,7 +858,15 @@ namespace OpenMD { MPI::COMM_WORLD.Allreduce(&ploc1, &ploc2, 1, MPI::REALTYPE, MPI::SUM); embeddingPot[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 } @@ -823,9 +909,25 @@ namespace OpenMD { 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; @@ -1007,16 +1109,14 @@ namespace OpenMD { idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); } + if (storageLayout_ & DataStorage::dslFlucQPosition) { + idat.flucQ1 = &(atomRowData.flucQPos[atom1]); + idat.flucQ2 = &(atomColData.flucQPos[atom2]); + } + #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]) ); if (storageLayout_ & DataStorage::dslAmat) { idat.A1 = &(snap_->atomData.aMat[atom1]); @@ -1057,6 +1157,12 @@ namespace OpenMD { 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 } @@ -1069,7 +1175,16 @@ namespace OpenMD { atomRowData.force[atom1] += *(idat.f1); atomColData.force[atom2] -= *(idat.f1); - // should particle pot be done here also? + if (storageLayout_ & DataStorage::dslFlucQForce) { + atomRowData.flucQFrc[atom1] -= *(idat.dVdFQ1); + atomColData.flucQFrc[atom2] -= *(idat.dVdFQ2); + } + + if (storageLayout_ & DataStorage::dslElectricField) { + atomRowData.electricField[atom1] += *(idat.eField1); + atomColData.electricField[atom2] += *(idat.eField2); + } + #else pairwisePot += *(idat.pot); @@ -1077,10 +1192,24 @@ namespace OpenMD { 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); + snap_->atomData.particlePot[atom2] += *(idat.vpair) * *(idat.sw); } - + + 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 }