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#include "math/SquareMatrix3.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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#include "brains/SnapshotManager.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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/** |
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* distributeInitialData is essentially a copy of the older fortran |
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* SimulationSetup |
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*/ |
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|
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void ForceMatrixDecomposition::distributeInitialData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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#ifdef IS_MPI |
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int nLocal = snap_->getNumberOfAtoms(); |
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int nGroups = snap_->getNumberOfCutoffGroups(); |
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|
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AtomCommIntRow = new Communicator<Row,int>(nLocal); |
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AtomCommRealRow = new Communicator<Row,RealType>(nLocal); |
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AtomCommVectorRow = new Communicator<Row,Vector3d>(nLocal); |
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AtomCommMatrixRow = new Communicator<Row,Mat3x3d>(nLocal); |
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|
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AtomCommIntColumn = new Communicator<Column,int>(nLocal); |
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AtomCommRealColumn = new Communicator<Column,RealType>(nLocal); |
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AtomCommVectorColumn = new Communicator<Column,Vector3d>(nLocal); |
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AtomCommMatrixColumn = new Communicator<Column,Mat3x3d>(nLocal); |
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|
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cgCommIntRow = new Communicator<Row,int>(nGroups); |
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cgCommVectorRow = new Communicator<Row,Vector3d>(nGroups); |
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cgCommIntColumn = new Communicator<Column,int>(nGroups); |
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cgCommVectorColumn = new Communicator<Column,Vector3d>(nGroups); |
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|
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int nAtomsInRow = AtomCommIntRow->getSize(); |
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int nAtomsInCol = AtomCommIntColumn->getSize(); |
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int nGroupsInRow = cgCommIntRow->getSize(); |
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int nGroupsInCol = cgCommIntColumn->getSize(); |
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|
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// Modify the data storage objects with the correct layouts and sizes: |
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atomRowData.resize(nAtomsInRow); |
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atomRowData.setStorageLayout(storageLayout_); |
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atomColData.resize(nAtomsInCol); |
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atomColData.setStorageLayout(storageLayout_); |
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cgRowData.resize(nGroupsInRow); |
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cgRowData.setStorageLayout(DataStorage::dslPosition); |
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cgColData.resize(nGroupsInCol); |
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cgColData.setStorageLayout(DataStorage::dslPosition); |
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|
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vector<vector<RealType> > pot_row(N_INTERACTION_FAMILIES, |
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vector<RealType> (nAtomsInRow, 0.0)); |
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vector<vector<RealType> > pot_col(N_INTERACTION_FAMILIES, |
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vector<RealType> (nAtomsInCol, 0.0)); |
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|
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|
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vector<RealType> pot_local(N_INTERACTION_FAMILIES, 0.0); |
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|
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// gather the information for atomtype IDs (atids): |
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vector<int> identsLocal = info_->getIdentArray(); |
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identsRow.reserve(nAtomsInRow); |
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identsCol.reserve(nAtomsInCol); |
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|
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AtomCommIntRow->gather(identsLocal, identsRow); |
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AtomCommIntColumn->gather(identsLocal, identsCol); |
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|
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AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
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AtomCommIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
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AtomCommIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
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|
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cgLocalToGlobal = info_->getGlobalGroupIndices(); |
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cgCommIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
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cgCommIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
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|
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// still need: |
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// topoDist |
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// exclude |
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#endif |
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} |
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|
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|
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|
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void ForceMatrixDecomposition::distributeData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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#ifdef IS_MPI |
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|
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// gather up the atomic positions |
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AtomCommVectorRow->gather(snap_->atomData.position, |
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atomRowData.position); |
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AtomCommVectorColumn->gather(snap_->atomData.position, |
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atomColData.position); |
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|
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// gather up the cutoff group positions |
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cgCommVectorRow->gather(snap_->cgData.position, |
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cgRowData.position); |
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cgCommVectorColumn->gather(snap_->cgData.position, |
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cgColData.position); |
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|
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// if needed, gather the atomic rotation matrices |
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if (storageLayout_ & DataStorage::dslAmat) { |
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AtomCommMatrixRow->gather(snap_->atomData.aMat, |
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atomRowData.aMat); |
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AtomCommMatrixColumn->gather(snap_->atomData.aMat, |
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atomColData.aMat); |
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} |
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|
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// if needed, gather the atomic eletrostatic frames |
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if (storageLayout_ & DataStorage::dslElectroFrame) { |
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AtomCommMatrixRow->gather(snap_->atomData.electroFrame, |
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atomRowData.electroFrame); |
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AtomCommMatrixColumn->gather(snap_->atomData.electroFrame, |
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atomColData.electroFrame); |
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} |
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#endif |
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} |
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|
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void ForceMatrixDecomposition::collectIntermediateData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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#ifdef IS_MPI |
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|
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if (storageLayout_ & DataStorage::dslDensity) { |
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|
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AtomCommRealRow->scatter(atomRowData.density, |
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snap_->atomData.density); |
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|
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int n = snap_->atomData.density.size(); |
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std::vector<RealType> rho_tmp(n, 0.0); |
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AtomCommRealColumn->scatter(atomColData.density, rho_tmp); |
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for (int i = 0; i < n; i++) |
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snap_->atomData.density[i] += rho_tmp[i]; |
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} |
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#endif |
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} |
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|
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void ForceMatrixDecomposition::distributeIntermediateData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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#ifdef IS_MPI |
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if (storageLayout_ & DataStorage::dslFunctional) { |
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AtomCommRealRow->gather(snap_->atomData.functional, |
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atomRowData.functional); |
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AtomCommRealColumn->gather(snap_->atomData.functional, |
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atomColData.functional); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
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AtomCommRealRow->gather(snap_->atomData.functionalDerivative, |
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atomRowData.functionalDerivative); |
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AtomCommRealColumn->gather(snap_->atomData.functionalDerivative, |
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atomColData.functionalDerivative); |
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} |
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#endif |
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} |
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|
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|
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void ForceMatrixDecomposition::collectData() { |
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snap_ = sman_->getCurrentSnapshot(); |
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storageLayout_ = sman_->getStorageLayout(); |
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#ifdef IS_MPI |
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int n = snap_->atomData.force.size(); |
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vector<Vector3d> frc_tmp(n, V3Zero); |
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|
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AtomCommVectorRow->scatter(atomRowData.force, frc_tmp); |
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for (int i = 0; i < n; i++) { |
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snap_->atomData.force[i] += frc_tmp[i]; |
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frc_tmp[i] = 0.0; |
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} |
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|
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AtomCommVectorColumn->scatter(atomColData.force, frc_tmp); |
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for (int i = 0; i < n; i++) |
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snap_->atomData.force[i] += frc_tmp[i]; |
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|
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|
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if (storageLayout_ & DataStorage::dslTorque) { |
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|
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int nt = snap_->atomData.force.size(); |
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vector<Vector3d> trq_tmp(nt, V3Zero); |
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|
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AtomCommVectorRow->scatter(atomRowData.torque, trq_tmp); |
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for (int i = 0; i < n; i++) { |
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snap_->atomData.torque[i] += trq_tmp[i]; |
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trq_tmp[i] = 0.0; |
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} |
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|
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AtomCommVectorColumn->scatter(atomColData.torque, trq_tmp); |
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for (int i = 0; i < n; i++) |
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snap_->atomData.torque[i] += trq_tmp[i]; |
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} |
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|
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int nLocal = snap_->getNumberOfAtoms(); |
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|
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vector<vector<RealType> > pot_temp(N_INTERACTION_FAMILIES, |
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vector<RealType> (nLocal, 0.0)); |
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|
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for (int i = 0; i < N_INTERACTION_FAMILIES; i++) { |
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AtomCommRealRow->scatter(pot_row[i], pot_temp[i]); |
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for (int ii = 0; ii < pot_temp[i].size(); ii++ ) { |
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pot_local[i] += pot_temp[i][ii]; |
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} |
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} |
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#endif |
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} |
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|
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|
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Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2){ |
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Vector3d d; |
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|
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#ifdef IS_MPI |
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d = cgColData.position[cg2] - cgRowData.position[cg1]; |
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#else |
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d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; |
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#endif |
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|
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snap_->wrapVector(d); |
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return d; |
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} |
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|
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|
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Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1){ |
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|
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Vector3d d; |
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|
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#ifdef IS_MPI |
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d = cgRowData.position[cg1] - atomRowData.position[atom1]; |
| 267 |
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#else |
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d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; |
| 269 |
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#endif |
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|
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snap_->wrapVector(d); |
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return d; |
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} |
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|
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Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2){ |
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Vector3d d; |
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|
| 278 |
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#ifdef IS_MPI |
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d = cgColData.position[cg2] - atomColData.position[atom2]; |
| 280 |
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#else |
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d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; |
| 282 |
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#endif |
| 283 |
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|
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snap_->wrapVector(d); |
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return d; |
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} |
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|
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Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2){ |
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Vector3d d; |
| 290 |
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|
| 291 |
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#ifdef IS_MPI |
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d = atomColData.position[atom2] - atomRowData.position[atom1]; |
| 293 |
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#else |
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d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; |
| 295 |
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#endif |
| 296 |
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|
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snap_->wrapVector(d); |
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return d; |
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} |
| 300 |
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|
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void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ |
| 302 |
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#ifdef IS_MPI |
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atomRowData.force[atom1] += fg; |
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#else |
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snap_->atomData.force[atom1] += fg; |
| 306 |
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#endif |
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} |
| 308 |
< |
|
| 309 |
< |
void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){ |
| 310 |
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#ifdef IS_MPI |
| 311 |
< |
atomColData.force[atom2] += fg; |
| 312 |
< |
#else |
| 313 |
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snap_->atomData.force[atom2] += fg; |
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#endif |
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|
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} |
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|
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// filling interaction blocks with pointers |
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InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
| 320 |
< |
|
| 321 |
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InteractionData idat; |
| 322 |
< |
#ifdef IS_MPI |
| 323 |
< |
if (storageLayout_ & DataStorage::dslAmat) { |
| 324 |
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idat.A1 = &(atomRowData.aMat[atom1]); |
| 325 |
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idat.A2 = &(atomColData.aMat[atom2]); |
| 326 |
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} |
| 327 |
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|
| 328 |
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if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 329 |
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idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
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idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
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} |
| 332 |
< |
|
| 333 |
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if (storageLayout_ & DataStorage::dslTorque) { |
| 334 |
< |
idat.t1 = &(atomRowData.torque[atom1]); |
| 335 |
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idat.t2 = &(atomColData.torque[atom2]); |
| 336 |
< |
} |
| 337 |
< |
|
| 338 |
< |
if (storageLayout_ & DataStorage::dslDensity) { |
| 339 |
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idat.rho1 = &(atomRowData.density[atom1]); |
| 340 |
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idat.rho2 = &(atomColData.density[atom2]); |
| 341 |
< |
} |
| 342 |
< |
|
| 343 |
< |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 344 |
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idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 345 |
< |
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 346 |
< |
} |
| 347 |
< |
#else |
| 348 |
< |
if (storageLayout_ & DataStorage::dslAmat) { |
| 349 |
< |
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 350 |
< |
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 351 |
< |
} |
| 352 |
< |
|
| 353 |
< |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 354 |
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idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 355 |
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idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 356 |
< |
} |
| 357 |
< |
|
| 358 |
< |
if (storageLayout_ & DataStorage::dslTorque) { |
| 359 |
< |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 360 |
< |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 361 |
< |
} |
| 362 |
< |
|
| 363 |
< |
if (storageLayout_ & DataStorage::dslDensity) { |
| 364 |
< |
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 365 |
< |
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 366 |
< |
} |
| 367 |
< |
|
| 368 |
< |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 369 |
< |
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 370 |
< |
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 371 |
< |
} |
| 372 |
< |
#endif |
| 373 |
< |
|
| 374 |
< |
} |
| 375 |
< |
InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
| 376 |
< |
InteractionData idat; |
| 377 |
< |
skippedCharge1 |
| 378 |
< |
skippedCharge2 |
| 379 |
< |
rij |
| 380 |
< |
d |
| 381 |
< |
electroMult |
| 382 |
< |
sw |
| 383 |
< |
f |
| 384 |
< |
#ifdef IS_MPI |
| 385 |
< |
|
| 386 |
< |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 387 |
< |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 388 |
< |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 389 |
< |
} |
| 390 |
< |
if (storageLayout_ & DataStorage::dslTorque) { |
| 391 |
< |
idat.t1 = &(atomRowData.torque[atom1]); |
| 392 |
< |
idat.t2 = &(atomColData.torque[atom2]); |
| 393 |
< |
} |
| 394 |
< |
|
| 395 |
< |
|
| 396 |
< |
} |
| 397 |
< |
SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
| 398 |
< |
} |
| 399 |
< |
|
| 400 |
< |
|
| 401 |
< |
/* |
| 402 |
< |
* buildNeighborList |
| 403 |
< |
* |
| 404 |
< |
* first element of pair is row-indexed CutoffGroup |
| 405 |
< |
* second element of pair is column-indexed CutoffGroup |
| 406 |
< |
*/ |
| 407 |
< |
vector<pair<int, int> > buildNeighborList() { |
| 408 |
< |
Vector3d dr, invWid, rs, shift; |
| 409 |
< |
Vector3i cc, m1v, m2s; |
| 410 |
< |
RealType rrNebr; |
| 411 |
< |
int c, j1, j2, m1, m1x, m1y, m1z, m2, n, offset; |
| 412 |
< |
|
| 413 |
< |
|
| 414 |
< |
vector<pair<int, int> > neighborList; |
| 415 |
< |
Vector3i nCells; |
| 416 |
< |
Vector3d invWid, r; |
| 417 |
< |
|
| 418 |
< |
rList_ = (rCut_ + skinThickness_); |
| 419 |
< |
rl2 = rList_ * rList_; |
| 420 |
< |
|
| 421 |
< |
snap_ = sman_->getCurrentSnapshot(); |
| 422 |
< |
Mat3x3d Hmat = snap_->getHmat(); |
| 423 |
< |
Vector3d Hx = Hmat.getColumn(0); |
| 424 |
< |
Vector3d Hy = Hmat.getColumn(1); |
| 425 |
< |
Vector3d Hz = Hmat.getColumn(2); |
| 426 |
< |
|
| 427 |
< |
nCells.x() = (int) ( Hx.length() )/ rList_; |
| 428 |
< |
nCells.y() = (int) ( Hy.length() )/ rList_; |
| 429 |
< |
nCells.z() = (int) ( Hz.length() )/ rList_; |
| 430 |
< |
|
| 431 |
< |
for (i = 0; i < nGroupsInRow; i++) { |
| 432 |
< |
rs = cgRowData.position[i]; |
| 433 |
< |
snap_->scaleVector(rs); |
| 434 |
< |
} |
| 435 |
< |
|
| 436 |
< |
|
| 437 |
< |
VDiv (invWid, cells, region); |
| 438 |
< |
for (n = nMol; n < nMol + cells.componentProduct(); n ++) cellList[n] = -1; |
| 439 |
< |
for (n = 0; n < nMol; n ++) { |
| 440 |
< |
VSAdd (rs, mol[n].r, 0.5, region); |
| 441 |
< |
VMul (cc, rs, invWid); |
| 442 |
< |
c = VLinear (cc, cells) + nMol; |
| 443 |
< |
cellList[n] = cellList[c]; |
| 444 |
< |
cellList[c] = n; |
| 445 |
< |
} |
| 446 |
< |
nebrTabLen = 0; |
| 447 |
< |
for (m1z = 0; m1z < cells.z(); m1z++) { |
| 448 |
< |
for (m1y = 0; m1y < cells.y(); m1y++) { |
| 449 |
< |
for (m1x = 0; m1x < cells.x(); m1x++) { |
| 450 |
< |
Vector3i m1v(m1x, m1y, m1z); |
| 451 |
< |
m1 = VLinear(m1v, cells) + nMol; |
| 452 |
< |
for (offset = 0; offset < nOffset_; offset++) { |
| 453 |
< |
m2v = m1v + cellOffsets_[offset]; |
| 454 |
< |
shift = V3Zero(); |
| 455 |
< |
|
| 456 |
< |
if (m2v.x() >= cells.x) { |
| 457 |
< |
m2v.x() = 0; |
| 458 |
< |
shift.x() = region.x(); |
| 459 |
< |
} else if (m2v.x() < 0) { |
| 460 |
< |
m2v.x() = cells.x() - 1; |
| 461 |
< |
shift.x() = - region.x(); |
| 462 |
< |
} |
| 463 |
< |
|
| 464 |
< |
if (m2v.y() >= cells.y()) { |
| 465 |
< |
m2v.y() = 0; |
| 466 |
< |
shift.y() = region.y(); |
| 467 |
< |
} else if (m2v.y() < 0) { |
| 468 |
< |
m2v.y() = cells.y() - 1; |
| 469 |
< |
shift.y() = - region.y(); |
| 470 |
< |
} |
| 471 |
< |
|
| 472 |
< |
m2 = VLinear (m2v, cells) + nMol; |
| 473 |
< |
for (j1 = cellList[m1]; j1 >= 0; j1 = cellList[j1]) { |
| 474 |
< |
for (j2 = cellList[m2]; j2 >= 0; j2 = cellList[j2]) { |
| 475 |
< |
if (m1 != m2 || j2 < j1) { |
| 476 |
< |
dr = mol[j1].r - mol[j2].r; |
| 477 |
< |
VSub (dr, mol[j1].r, mol[j2].r); |
| 478 |
< |
VVSub (dr, shift); |
| 479 |
< |
if (VLenSq (dr) < rrNebr) { |
| 480 |
< |
neighborList.push_back(make_pair(j1, j2)); |
| 481 |
< |
} |
| 482 |
< |
} |
| 483 |
< |
} |
| 484 |
< |
} |
| 485 |
< |
} |
| 486 |
< |
} |
| 487 |
< |
} |
| 488 |
< |
} |
| 489 |
< |
} |
| 490 |
< |
|
| 491 |
< |
|
| 45 |
> |
#include "brains/PairList.hpp" |
| 46 |
> |
#include "primitives/Molecule.hpp" |
| 47 |
> |
|
| 48 |
> |
using namespace std; |
| 49 |
> |
namespace OpenMD { |
| 50 |
> |
|
| 51 |
> |
ForceMatrixDecomposition::ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : |
| 52 |
> |
ForceDecomposition(info, iMan) { |
| 53 |
> |
// In a parallel computation, row and colum scans must visit all |
| 54 |
> |
// surrounding cells (not just the 14 upper triangular blocks that |
| 55 |
> |
// are used when the processor can see all pairs) |
| 56 |
> |
#ifdef IS_MPI |
| 57 |
> |
cellOffsets_.push_back( Vector3i(-1, 0, 0) ); |
| 58 |
> |
cellOffsets_.push_back( Vector3i(-1,-1, 0) ); |
| 59 |
> |
cellOffsets_.push_back( Vector3i( 0,-1, 0) ); |
| 60 |
> |
cellOffsets_.push_back( Vector3i( 1,-1, 0) ); |
| 61 |
> |
cellOffsets_.push_back( Vector3i( 0, 0,-1) ); |
| 62 |
> |
cellOffsets_.push_back( Vector3i(-1, 0, 1) ); |
| 63 |
> |
cellOffsets_.push_back( Vector3i(-1,-1,-1) ); |
| 64 |
> |
cellOffsets_.push_back( Vector3i( 0,-1,-1) ); |
| 65 |
> |
cellOffsets_.push_back( Vector3i( 1,-1,-1) ); |
| 66 |
> |
cellOffsets_.push_back( Vector3i( 1, 0,-1) ); |
| 67 |
> |
cellOffsets_.push_back( Vector3i( 1, 1,-1) ); |
| 68 |
> |
cellOffsets_.push_back( Vector3i( 0, 1,-1) ); |
| 69 |
> |
cellOffsets_.push_back( Vector3i(-1, 1,-1) ); |
| 70 |
> |
#endif |
| 71 |
> |
} |
| 72 |
> |
|
| 73 |
> |
/** |
| 74 |
> |
* distributeInitialData is essentially a copy of the older fortran |
| 75 |
> |
* SimulationSetup |
| 76 |
> |
*/ |
| 77 |
> |
void ForceMatrixDecomposition::distributeInitialData() { |
| 78 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 79 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 80 |
> |
ff_ = info_->getForceField(); |
| 81 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 82 |
> |
|
| 83 |
> |
nGroups_ = info_->getNLocalCutoffGroups(); |
| 84 |
> |
// gather the information for atomtype IDs (atids): |
| 85 |
> |
idents = info_->getIdentArray(); |
| 86 |
> |
AtomLocalToGlobal = info_->getGlobalAtomIndices(); |
| 87 |
> |
cgLocalToGlobal = info_->getGlobalGroupIndices(); |
| 88 |
> |
vector<int> globalGroupMembership = info_->getGlobalGroupMembership(); |
| 89 |
> |
|
| 90 |
> |
massFactors = info_->getMassFactors(); |
| 91 |
> |
|
| 92 |
> |
PairList* excludes = info_->getExcludedInteractions(); |
| 93 |
> |
PairList* oneTwo = info_->getOneTwoInteractions(); |
| 94 |
> |
PairList* oneThree = info_->getOneThreeInteractions(); |
| 95 |
> |
PairList* oneFour = info_->getOneFourInteractions(); |
| 96 |
> |
|
| 97 |
> |
#ifdef IS_MPI |
| 98 |
> |
|
| 99 |
> |
MPI::Intracomm row = rowComm.getComm(); |
| 100 |
> |
MPI::Intracomm col = colComm.getComm(); |
| 101 |
> |
|
| 102 |
> |
AtomPlanIntRow = new Plan<int>(row, nLocal_); |
| 103 |
> |
AtomPlanRealRow = new Plan<RealType>(row, nLocal_); |
| 104 |
> |
AtomPlanVectorRow = new Plan<Vector3d>(row, nLocal_); |
| 105 |
> |
AtomPlanMatrixRow = new Plan<Mat3x3d>(row, nLocal_); |
| 106 |
> |
AtomPlanPotRow = new Plan<potVec>(row, nLocal_); |
| 107 |
> |
|
| 108 |
> |
AtomPlanIntColumn = new Plan<int>(col, nLocal_); |
| 109 |
> |
AtomPlanRealColumn = new Plan<RealType>(col, nLocal_); |
| 110 |
> |
AtomPlanVectorColumn = new Plan<Vector3d>(col, nLocal_); |
| 111 |
> |
AtomPlanMatrixColumn = new Plan<Mat3x3d>(col, nLocal_); |
| 112 |
> |
AtomPlanPotColumn = new Plan<potVec>(col, nLocal_); |
| 113 |
> |
|
| 114 |
> |
cgPlanIntRow = new Plan<int>(row, nGroups_); |
| 115 |
> |
cgPlanVectorRow = new Plan<Vector3d>(row, nGroups_); |
| 116 |
> |
cgPlanIntColumn = new Plan<int>(col, nGroups_); |
| 117 |
> |
cgPlanVectorColumn = new Plan<Vector3d>(col, nGroups_); |
| 118 |
> |
|
| 119 |
> |
nAtomsInRow_ = AtomPlanIntRow->getSize(); |
| 120 |
> |
nAtomsInCol_ = AtomPlanIntColumn->getSize(); |
| 121 |
> |
nGroupsInRow_ = cgPlanIntRow->getSize(); |
| 122 |
> |
nGroupsInCol_ = cgPlanIntColumn->getSize(); |
| 123 |
> |
|
| 124 |
> |
// Modify the data storage objects with the correct layouts and sizes: |
| 125 |
> |
atomRowData.resize(nAtomsInRow_); |
| 126 |
> |
atomRowData.setStorageLayout(storageLayout_); |
| 127 |
> |
atomColData.resize(nAtomsInCol_); |
| 128 |
> |
atomColData.setStorageLayout(storageLayout_); |
| 129 |
> |
cgRowData.resize(nGroupsInRow_); |
| 130 |
> |
cgRowData.setStorageLayout(DataStorage::dslPosition); |
| 131 |
> |
cgColData.resize(nGroupsInCol_); |
| 132 |
> |
cgColData.setStorageLayout(DataStorage::dslPosition); |
| 133 |
> |
|
| 134 |
> |
identsRow.resize(nAtomsInRow_); |
| 135 |
> |
identsCol.resize(nAtomsInCol_); |
| 136 |
> |
|
| 137 |
> |
AtomPlanIntRow->gather(idents, identsRow); |
| 138 |
> |
AtomPlanIntColumn->gather(idents, identsCol); |
| 139 |
> |
|
| 140 |
> |
// allocate memory for the parallel objects |
| 141 |
> |
atypesRow.resize(nAtomsInRow_); |
| 142 |
> |
atypesCol.resize(nAtomsInCol_); |
| 143 |
> |
|
| 144 |
> |
for (int i = 0; i < nAtomsInRow_; i++) |
| 145 |
> |
atypesRow[i] = ff_->getAtomType(identsRow[i]); |
| 146 |
> |
for (int i = 0; i < nAtomsInCol_; i++) |
| 147 |
> |
atypesCol[i] = ff_->getAtomType(identsCol[i]); |
| 148 |
> |
|
| 149 |
> |
pot_row.resize(nAtomsInRow_); |
| 150 |
> |
pot_col.resize(nAtomsInCol_); |
| 151 |
> |
|
| 152 |
> |
AtomRowToGlobal.resize(nAtomsInRow_); |
| 153 |
> |
AtomColToGlobal.resize(nAtomsInCol_); |
| 154 |
> |
AtomPlanIntRow->gather(AtomLocalToGlobal, AtomRowToGlobal); |
| 155 |
> |
AtomPlanIntColumn->gather(AtomLocalToGlobal, AtomColToGlobal); |
| 156 |
> |
|
| 157 |
> |
cerr << "Atoms in Local:\n"; |
| 158 |
> |
for (int i = 0; i < AtomLocalToGlobal.size(); i++) |
| 159 |
> |
{ |
| 160 |
> |
cerr << "i =\t" << i << "\t localAt =\t" << AtomLocalToGlobal[i] << "\n"; |
| 161 |
> |
} |
| 162 |
> |
cerr << "Atoms in Row:\n"; |
| 163 |
> |
for (int i = 0; i < AtomRowToGlobal.size(); i++) |
| 164 |
> |
{ |
| 165 |
> |
cerr << "i =\t" << i << "\t rowAt =\t" << AtomRowToGlobal[i] << "\n"; |
| 166 |
> |
} |
| 167 |
> |
cerr << "Atoms in Col:\n"; |
| 168 |
> |
for (int i = 0; i < AtomColToGlobal.size(); i++) |
| 169 |
> |
{ |
| 170 |
> |
cerr << "i =\t" << i << "\t colAt =\t" << AtomColToGlobal[i] << "\n"; |
| 171 |
> |
} |
| 172 |
> |
|
| 173 |
> |
cgRowToGlobal.resize(nGroupsInRow_); |
| 174 |
> |
cgColToGlobal.resize(nGroupsInCol_); |
| 175 |
> |
cgPlanIntRow->gather(cgLocalToGlobal, cgRowToGlobal); |
| 176 |
> |
cgPlanIntColumn->gather(cgLocalToGlobal, cgColToGlobal); |
| 177 |
> |
|
| 178 |
> |
cerr << "Gruops in Local:\n"; |
| 179 |
> |
for (int i = 0; i < cgLocalToGlobal.size(); i++) |
| 180 |
> |
{ |
| 181 |
> |
cerr << "i =\t" << i << "\t localCG =\t" << cgLocalToGlobal[i] << "\n"; |
| 182 |
> |
} |
| 183 |
> |
cerr << "Groups in Row:\n"; |
| 184 |
> |
for (int i = 0; i < cgRowToGlobal.size(); i++) |
| 185 |
> |
{ |
| 186 |
> |
cerr << "i =\t" << i << "\t rowCG =\t" << cgRowToGlobal[i] << "\n"; |
| 187 |
> |
} |
| 188 |
> |
cerr << "Groups in Col:\n"; |
| 189 |
> |
for (int i = 0; i < cgColToGlobal.size(); i++) |
| 190 |
> |
{ |
| 191 |
> |
cerr << "i =\t" << i << "\t colCG =\t" << cgColToGlobal[i] << "\n"; |
| 192 |
> |
} |
| 193 |
> |
|
| 194 |
> |
massFactorsRow.resize(nAtomsInRow_); |
| 195 |
> |
massFactorsCol.resize(nAtomsInCol_); |
| 196 |
> |
AtomPlanRealRow->gather(massFactors, massFactorsRow); |
| 197 |
> |
AtomPlanRealColumn->gather(massFactors, massFactorsCol); |
| 198 |
> |
|
| 199 |
> |
groupListRow_.clear(); |
| 200 |
> |
groupListRow_.resize(nGroupsInRow_); |
| 201 |
> |
for (int i = 0; i < nGroupsInRow_; i++) |
| 202 |
> |
{ |
| 203 |
> |
int gid = cgRowToGlobal[i]; |
| 204 |
> |
for (int j = 0; j < nAtomsInRow_; j++) |
| 205 |
> |
{ |
| 206 |
> |
int aid = AtomRowToGlobal[j]; |
| 207 |
> |
if (globalGroupMembership[aid] == gid) |
| 208 |
> |
groupListRow_[i].push_back(j); |
| 209 |
> |
} |
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
groupListCol_.clear(); |
| 213 |
> |
groupListCol_.resize(nGroupsInCol_); |
| 214 |
> |
for (int i = 0; i < nGroupsInCol_; i++) |
| 215 |
> |
{ |
| 216 |
> |
int gid = cgColToGlobal[i]; |
| 217 |
> |
for (int j = 0; j < nAtomsInCol_; j++) |
| 218 |
> |
{ |
| 219 |
> |
int aid = AtomColToGlobal[j]; |
| 220 |
> |
if (globalGroupMembership[aid] == gid) |
| 221 |
> |
groupListCol_[i].push_back(j); |
| 222 |
> |
} |
| 223 |
> |
} |
| 224 |
> |
|
| 225 |
> |
excludesForAtom.clear(); |
| 226 |
> |
excludesForAtom.resize(nAtomsInRow_); |
| 227 |
> |
toposForAtom.clear(); |
| 228 |
> |
toposForAtom.resize(nAtomsInRow_); |
| 229 |
> |
topoDist.clear(); |
| 230 |
> |
topoDist.resize(nAtomsInRow_); |
| 231 |
> |
for (int i = 0; i < nAtomsInRow_; i++) |
| 232 |
> |
{ |
| 233 |
> |
int iglob = AtomRowToGlobal[i]; |
| 234 |
> |
|
| 235 |
> |
for (int j = 0; j < nAtomsInCol_; j++) |
| 236 |
> |
{ |
| 237 |
> |
int jglob = AtomColToGlobal[j]; |
| 238 |
> |
|
| 239 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 240 |
> |
excludesForAtom[i].push_back(j); |
| 241 |
> |
|
| 242 |
> |
if (oneTwo->hasPair(iglob, jglob)) |
| 243 |
> |
{ |
| 244 |
> |
toposForAtom[i].push_back(j); |
| 245 |
> |
topoDist[i].push_back(1); |
| 246 |
> |
} else |
| 247 |
> |
{ |
| 248 |
> |
if (oneThree->hasPair(iglob, jglob)) |
| 249 |
> |
{ |
| 250 |
> |
toposForAtom[i].push_back(j); |
| 251 |
> |
topoDist[i].push_back(2); |
| 252 |
> |
} else |
| 253 |
> |
{ |
| 254 |
> |
if (oneFour->hasPair(iglob, jglob)) |
| 255 |
> |
{ |
| 256 |
> |
toposForAtom[i].push_back(j); |
| 257 |
> |
topoDist[i].push_back(3); |
| 258 |
> |
} |
| 259 |
> |
} |
| 260 |
> |
} |
| 261 |
> |
} |
| 262 |
> |
} |
| 263 |
> |
|
| 264 |
> |
#endif |
| 265 |
> |
|
| 266 |
> |
// allocate memory for the parallel objects |
| 267 |
> |
atypesLocal.resize(nLocal_); |
| 268 |
> |
|
| 269 |
> |
for (int i = 0; i < nLocal_; i++) |
| 270 |
> |
atypesLocal[i] = ff_->getAtomType(idents[i]); |
| 271 |
> |
|
| 272 |
> |
groupList_.clear(); |
| 273 |
> |
groupList_.resize(nGroups_); |
| 274 |
> |
for (int i = 0; i < nGroups_; i++) |
| 275 |
> |
{ |
| 276 |
> |
int gid = cgLocalToGlobal[i]; |
| 277 |
> |
for (int j = 0; j < nLocal_; j++) |
| 278 |
> |
{ |
| 279 |
> |
int aid = AtomLocalToGlobal[j]; |
| 280 |
> |
if (globalGroupMembership[aid] == gid) |
| 281 |
> |
{ |
| 282 |
> |
groupList_[i].push_back(j); |
| 283 |
> |
} |
| 284 |
> |
} |
| 285 |
> |
} |
| 286 |
> |
|
| 287 |
> |
excludesForAtom.clear(); |
| 288 |
> |
excludesForAtom.resize(nLocal_); |
| 289 |
> |
toposForAtom.clear(); |
| 290 |
> |
toposForAtom.resize(nLocal_); |
| 291 |
> |
topoDist.clear(); |
| 292 |
> |
topoDist.resize(nLocal_); |
| 293 |
> |
|
| 294 |
> |
for (int i = 0; i < nLocal_; i++) |
| 295 |
> |
{ |
| 296 |
> |
int iglob = AtomLocalToGlobal[i]; |
| 297 |
> |
|
| 298 |
> |
for (int j = 0; j < nLocal_; j++) |
| 299 |
> |
{ |
| 300 |
> |
int jglob = AtomLocalToGlobal[j]; |
| 301 |
> |
|
| 302 |
> |
if (excludes->hasPair(iglob, jglob)) |
| 303 |
> |
excludesForAtom[i].push_back(j); |
| 304 |
> |
|
| 305 |
> |
if (oneTwo->hasPair(iglob, jglob)) |
| 306 |
> |
{ |
| 307 |
> |
toposForAtom[i].push_back(j); |
| 308 |
> |
topoDist[i].push_back(1); |
| 309 |
> |
} else |
| 310 |
> |
{ |
| 311 |
> |
if (oneThree->hasPair(iglob, jglob)) |
| 312 |
> |
{ |
| 313 |
> |
toposForAtom[i].push_back(j); |
| 314 |
> |
topoDist[i].push_back(2); |
| 315 |
> |
} else |
| 316 |
> |
{ |
| 317 |
> |
if (oneFour->hasPair(iglob, jglob)) |
| 318 |
> |
{ |
| 319 |
> |
toposForAtom[i].push_back(j); |
| 320 |
> |
topoDist[i].push_back(3); |
| 321 |
> |
} |
| 322 |
> |
} |
| 323 |
> |
} |
| 324 |
> |
} |
| 325 |
> |
} |
| 326 |
> |
|
| 327 |
> |
Globals* simParams_ = info_->getSimParams(); |
| 328 |
> |
if (simParams_->haveNeighborListReorderFreq()) |
| 329 |
> |
{ |
| 330 |
> |
neighborListReorderFreq = simParams_->getNeighborListReorderFreq(); |
| 331 |
> |
} else |
| 332 |
> |
{ |
| 333 |
> |
neighborListReorderFreq = 0; |
| 334 |
> |
} |
| 335 |
> |
reorderFreqCounter = 1; |
| 336 |
> |
|
| 337 |
> |
createGtypeCutoffMap(); |
| 338 |
> |
|
| 339 |
> |
} |
| 340 |
> |
|
| 341 |
> |
void ForceMatrixDecomposition::createGtypeCutoffMap() { |
| 342 |
> |
|
| 343 |
> |
RealType tol = 1e-6; |
| 344 |
> |
largestRcut_ = 0.0; |
| 345 |
> |
RealType rc; |
| 346 |
> |
int atid; |
| 347 |
> |
set<AtomType*> atypes = info_->getSimulatedAtomTypes(); |
| 348 |
> |
|
| 349 |
> |
map<int, RealType> atypeCutoff; |
| 350 |
> |
|
| 351 |
> |
for (set<AtomType*>::iterator at = atypes.begin(); at != atypes.end(); ++at) |
| 352 |
> |
{ |
| 353 |
> |
atid = (*at)->getIdent(); |
| 354 |
> |
if (userChoseCutoff_) |
| 355 |
> |
atypeCutoff[atid] = userCutoff_; |
| 356 |
> |
else |
| 357 |
> |
atypeCutoff[atid] = interactionMan_->getSuggestedCutoffRadius(*at); |
| 358 |
> |
} |
| 359 |
> |
|
| 360 |
> |
vector<RealType> gTypeCutoffs; |
| 361 |
> |
// first we do a single loop over the cutoff groups to find the |
| 362 |
> |
// largest cutoff for any atypes present in this group. |
| 363 |
> |
#ifdef IS_MPI |
| 364 |
> |
vector<RealType> groupCutoffRow(nGroupsInRow_, 0.0); |
| 365 |
> |
groupRowToGtype.resize(nGroupsInRow_); |
| 366 |
> |
for (int cg1 = 0; cg1 < nGroupsInRow_; cg1++) |
| 367 |
> |
{ |
| 368 |
> |
vector<int> atomListRow = getAtomsInGroupRow(cg1); |
| 369 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 370 |
> |
ia != atomListRow.end(); ++ia) |
| 371 |
> |
{ |
| 372 |
> |
int atom1 = (*ia); |
| 373 |
> |
atid = identsRow[atom1]; |
| 374 |
> |
if (atypeCutoff[atid] > groupCutoffRow[cg1]) |
| 375 |
> |
{ |
| 376 |
> |
groupCutoffRow[cg1] = atypeCutoff[atid]; |
| 377 |
> |
} |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
bool gTypeFound = false; |
| 381 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) |
| 382 |
> |
{ |
| 383 |
> |
if (abs(groupCutoffRow[cg1] - gTypeCutoffs[gt]) < tol) |
| 384 |
> |
{ |
| 385 |
> |
groupRowToGtype[cg1] = gt; |
| 386 |
> |
gTypeFound = true; |
| 387 |
> |
} |
| 388 |
> |
} |
| 389 |
> |
if (!gTypeFound) |
| 390 |
> |
{ |
| 391 |
> |
gTypeCutoffs.push_back( groupCutoffRow[cg1] ); |
| 392 |
> |
groupRowToGtype[cg1] = gTypeCutoffs.size() - 1; |
| 393 |
> |
} |
| 394 |
> |
|
| 395 |
> |
} |
| 396 |
> |
vector<RealType> groupCutoffCol(nGroupsInCol_, 0.0); |
| 397 |
> |
groupColToGtype.resize(nGroupsInCol_); |
| 398 |
> |
for (int cg2 = 0; cg2 < nGroupsInCol_; cg2++) |
| 399 |
> |
{ |
| 400 |
> |
vector<int> atomListCol = getAtomsInGroupColumn(cg2); |
| 401 |
> |
for (vector<int>::iterator jb = atomListCol.begin(); |
| 402 |
> |
jb != atomListCol.end(); ++jb) |
| 403 |
> |
{ |
| 404 |
> |
int atom2 = (*jb); |
| 405 |
> |
atid = identsCol[atom2]; |
| 406 |
> |
if (atypeCutoff[atid] > groupCutoffCol[cg2]) |
| 407 |
> |
{ |
| 408 |
> |
groupCutoffCol[cg2] = atypeCutoff[atid]; |
| 409 |
> |
} |
| 410 |
> |
} |
| 411 |
> |
bool gTypeFound = false; |
| 412 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) |
| 413 |
> |
{ |
| 414 |
> |
if (abs(groupCutoffCol[cg2] - gTypeCutoffs[gt]) < tol) |
| 415 |
> |
{ |
| 416 |
> |
groupColToGtype[cg2] = gt; |
| 417 |
> |
gTypeFound = true; |
| 418 |
> |
} |
| 419 |
> |
} |
| 420 |
> |
if (!gTypeFound) |
| 421 |
> |
{ |
| 422 |
> |
gTypeCutoffs.push_back( groupCutoffCol[cg2] ); |
| 423 |
> |
groupColToGtype[cg2] = gTypeCutoffs.size() - 1; |
| 424 |
> |
} |
| 425 |
> |
} |
| 426 |
> |
#else |
| 427 |
> |
|
| 428 |
> |
vector<RealType> groupCutoff(nGroups_, 0.0); |
| 429 |
> |
groupToGtype.resize(nGroups_); |
| 430 |
> |
for (int cg1 = 0; cg1 < nGroups_; cg1++) |
| 431 |
> |
{ |
| 432 |
> |
groupCutoff[cg1] = 0.0; |
| 433 |
> |
vector<int> atomList = getAtomsInGroupRow(cg1); |
| 434 |
> |
for (vector<int>::iterator ia = atomList.begin(); ia != atomList.end(); ++ia) |
| 435 |
> |
{ |
| 436 |
> |
int atom1 = (*ia); |
| 437 |
> |
atid = idents[atom1]; |
| 438 |
> |
if (atypeCutoff[atid] > groupCutoff[cg1]) |
| 439 |
> |
groupCutoff[cg1] = atypeCutoff[atid]; |
| 440 |
> |
} |
| 441 |
> |
|
| 442 |
> |
bool gTypeFound = false; |
| 443 |
> |
for (int gt = 0; gt < gTypeCutoffs.size(); gt++) |
| 444 |
> |
{ |
| 445 |
> |
if (abs(groupCutoff[cg1] - gTypeCutoffs[gt]) < tol) |
| 446 |
> |
{ |
| 447 |
> |
groupToGtype[cg1] = gt; |
| 448 |
> |
gTypeFound = true; |
| 449 |
> |
} |
| 450 |
> |
} |
| 451 |
> |
if (!gTypeFound) |
| 452 |
> |
{ |
| 453 |
> |
gTypeCutoffs.push_back(groupCutoff[cg1]); |
| 454 |
> |
groupToGtype[cg1] = gTypeCutoffs.size() - 1; |
| 455 |
> |
} |
| 456 |
> |
} |
| 457 |
> |
#endif |
| 458 |
> |
|
| 459 |
> |
// Now we find the maximum group cutoff value present in the simulation |
| 460 |
> |
|
| 461 |
> |
RealType groupMax = *max_element(gTypeCutoffs.begin(), gTypeCutoffs.end()); |
| 462 |
> |
|
| 463 |
> |
#ifdef IS_MPI |
| 464 |
> |
MPI::COMM_WORLD.Allreduce(&groupMax, &groupMax, 1, MPI::REALTYPE, |
| 465 |
> |
MPI::MAX); |
| 466 |
> |
#endif |
| 467 |
> |
|
| 468 |
> |
RealType tradRcut = groupMax; |
| 469 |
> |
|
| 470 |
> |
for (int i = 0; i < gTypeCutoffs.size(); i++) |
| 471 |
> |
{ |
| 472 |
> |
for (int j = 0; j < gTypeCutoffs.size(); j++) |
| 473 |
> |
{ |
| 474 |
> |
RealType thisRcut; |
| 475 |
> |
switch (cutoffPolicy_) { |
| 476 |
> |
case TRADITIONAL: |
| 477 |
> |
thisRcut = tradRcut; |
| 478 |
> |
break; |
| 479 |
> |
case MIX: |
| 480 |
> |
thisRcut = 0.5 * (gTypeCutoffs[i] + gTypeCutoffs[j]); |
| 481 |
> |
break; |
| 482 |
> |
case MAX: |
| 483 |
> |
thisRcut = max(gTypeCutoffs[i], gTypeCutoffs[j]); |
| 484 |
> |
break; |
| 485 |
> |
default: |
| 486 |
> |
sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap " |
| 487 |
> |
"hit an unknown cutoff policy!\n"); |
| 488 |
> |
painCave.severity = OPENMD_ERROR; |
| 489 |
> |
painCave.isFatal = 1; |
| 490 |
> |
simError(); |
| 491 |
> |
break; |
| 492 |
> |
} |
| 493 |
> |
|
| 494 |
> |
pair<int, int> key = make_pair(i, j); |
| 495 |
> |
gTypeCutoffMap[key].first = thisRcut; |
| 496 |
> |
if (thisRcut > largestRcut_) |
| 497 |
> |
largestRcut_ = thisRcut; |
| 498 |
> |
gTypeCutoffMap[key].second = thisRcut * thisRcut; |
| 499 |
> |
gTypeCutoffMap[key].third = pow(thisRcut + skinThickness_, 2); |
| 500 |
> |
// sanity check |
| 501 |
> |
|
| 502 |
> |
if (userChoseCutoff_) |
| 503 |
> |
{ |
| 504 |
> |
if (abs(gTypeCutoffMap[key].first - userCutoff_) > 0.0001) |
| 505 |
> |
{ |
| 506 |
> |
sprintf(painCave.errMsg, "ForceMatrixDecomposition::createGtypeCutoffMap " |
| 507 |
> |
"user-specified rCut (%lf) does not match computed group Cutoff\n", userCutoff_); |
| 508 |
> |
painCave.severity = OPENMD_ERROR; |
| 509 |
> |
painCave.isFatal = 1; |
| 510 |
> |
simError(); |
| 511 |
> |
} |
| 512 |
> |
} |
| 513 |
> |
} |
| 514 |
> |
} |
| 515 |
> |
} |
| 516 |
> |
|
| 517 |
> |
groupCutoffs ForceMatrixDecomposition::getGroupCutoffs(int cg1, int cg2) { |
| 518 |
> |
int i, j; |
| 519 |
> |
#ifdef IS_MPI |
| 520 |
> |
i = groupRowToGtype[cg1]; |
| 521 |
> |
j = groupColToGtype[cg2]; |
| 522 |
> |
#else |
| 523 |
> |
i = groupToGtype[cg1]; |
| 524 |
> |
j = groupToGtype[cg2]; |
| 525 |
> |
#endif |
| 526 |
> |
return gTypeCutoffMap[make_pair(i, j)]; |
| 527 |
> |
} |
| 528 |
> |
|
| 529 |
> |
int ForceMatrixDecomposition::getTopologicalDistance(int atom1, int atom2) { |
| 530 |
> |
for (int j = 0; j < toposForAtom[atom1].size(); j++) |
| 531 |
> |
{ |
| 532 |
> |
if (toposForAtom[atom1][j] == atom2) |
| 533 |
> |
return topoDist[atom1][j]; |
| 534 |
> |
} |
| 535 |
> |
return 0; |
| 536 |
> |
} |
| 537 |
> |
|
| 538 |
> |
void ForceMatrixDecomposition::zeroWorkArrays() { |
| 539 |
> |
pairwisePot = 0.0; |
| 540 |
> |
embeddingPot = 0.0; |
| 541 |
> |
|
| 542 |
> |
#ifdef IS_MPI |
| 543 |
> |
if (storageLayout_ & DataStorage::dslForce) |
| 544 |
> |
{ |
| 545 |
> |
fill(atomRowData.force.begin(), atomRowData.force.end(), V3Zero); |
| 546 |
> |
fill(atomColData.force.begin(), atomColData.force.end(), V3Zero); |
| 547 |
> |
} |
| 548 |
> |
|
| 549 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 550 |
> |
{ |
| 551 |
> |
fill(atomRowData.torque.begin(), atomRowData.torque.end(), V3Zero); |
| 552 |
> |
fill(atomColData.torque.begin(), atomColData.torque.end(), V3Zero); |
| 553 |
> |
} |
| 554 |
> |
|
| 555 |
> |
fill(pot_row.begin(), pot_row.end(), |
| 556 |
> |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 557 |
> |
|
| 558 |
> |
fill(pot_col.begin(), pot_col.end(), |
| 559 |
> |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 560 |
> |
|
| 561 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 562 |
> |
{ |
| 563 |
> |
fill(atomRowData.particlePot.begin(), atomRowData.particlePot.end(), |
| 564 |
> |
0.0); |
| 565 |
> |
fill(atomColData.particlePot.begin(), atomColData.particlePot.end(), |
| 566 |
> |
0.0); |
| 567 |
> |
} |
| 568 |
> |
|
| 569 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 570 |
> |
{ |
| 571 |
> |
fill(atomRowData.density.begin(), atomRowData.density.end(), 0.0); |
| 572 |
> |
fill(atomColData.density.begin(), atomColData.density.end(), 0.0); |
| 573 |
> |
} |
| 574 |
> |
|
| 575 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 576 |
> |
{ |
| 577 |
> |
fill(atomRowData.functional.begin(), atomRowData.functional.end(), |
| 578 |
> |
0.0); |
| 579 |
> |
fill(atomColData.functional.begin(), atomColData.functional.end(), |
| 580 |
> |
0.0); |
| 581 |
> |
} |
| 582 |
> |
|
| 583 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 584 |
> |
{ |
| 585 |
> |
fill(atomRowData.functionalDerivative.begin(), |
| 586 |
> |
atomRowData.functionalDerivative.end(), 0.0); |
| 587 |
> |
fill(atomColData.functionalDerivative.begin(), |
| 588 |
> |
atomColData.functionalDerivative.end(), 0.0); |
| 589 |
> |
} |
| 590 |
> |
|
| 591 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 592 |
> |
{ |
| 593 |
> |
fill(atomRowData.skippedCharge.begin(), |
| 594 |
> |
atomRowData.skippedCharge.end(), 0.0); |
| 595 |
> |
fill(atomColData.skippedCharge.begin(), |
| 596 |
> |
atomColData.skippedCharge.end(), 0.0); |
| 597 |
> |
} |
| 598 |
> |
|
| 599 |
> |
#endif |
| 600 |
> |
// even in parallel, we need to zero out the local arrays: |
| 601 |
> |
|
| 602 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 603 |
> |
{ |
| 604 |
> |
fill(snap_->atomData.particlePot.begin(), snap_->atomData.particlePot.end(), 0.0); |
| 605 |
> |
} |
| 606 |
> |
|
| 607 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 608 |
> |
{ |
| 609 |
> |
fill(snap_->atomData.density.begin(), snap_->atomData.density.end(), 0.0); |
| 610 |
> |
} |
| 611 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 612 |
> |
{ |
| 613 |
> |
fill(snap_->atomData.functional.begin(), snap_->atomData.functional.end(), 0.0); |
| 614 |
> |
} |
| 615 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 616 |
> |
{ |
| 617 |
> |
fill(snap_->atomData.functionalDerivative.begin(), snap_->atomData.functionalDerivative.end(), 0.0); |
| 618 |
> |
} |
| 619 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 620 |
> |
{ |
| 621 |
> |
fill(snap_->atomData.skippedCharge.begin(), snap_->atomData.skippedCharge.end(), 0.0); |
| 622 |
> |
} |
| 623 |
> |
|
| 624 |
> |
} |
| 625 |
> |
|
| 626 |
> |
void ForceMatrixDecomposition::distributeData() { |
| 627 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 628 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 629 |
> |
#ifdef IS_MPI |
| 630 |
> |
|
| 631 |
> |
// gather up the atomic positions |
| 632 |
> |
AtomPlanVectorRow->gather(snap_->atomData.position, |
| 633 |
> |
atomRowData.position); |
| 634 |
> |
AtomPlanVectorColumn->gather(snap_->atomData.position, |
| 635 |
> |
atomColData.position); |
| 636 |
> |
|
| 637 |
> |
// gather up the cutoff group positions |
| 638 |
> |
|
| 639 |
> |
cerr << "before gather\n"; |
| 640 |
> |
for (int i = 0; i < snap_->cgData.position.size(); i++) |
| 641 |
> |
{ |
| 642 |
> |
cerr << "cgpos = " << snap_->cgData.position[i] << "\n"; |
| 643 |
> |
} |
| 644 |
> |
|
| 645 |
> |
cgPlanVectorRow->gather(snap_->cgData.position, |
| 646 |
> |
cgRowData.position); |
| 647 |
> |
|
| 648 |
> |
cerr << "after gather\n"; |
| 649 |
> |
for (int i = 0; i < cgRowData.position.size(); i++) |
| 650 |
> |
{ |
| 651 |
> |
cerr << "cgRpos = " << cgRowData.position[i] << "\n"; |
| 652 |
> |
} |
| 653 |
> |
|
| 654 |
> |
cgPlanVectorColumn->gather(snap_->cgData.position, |
| 655 |
> |
cgColData.position); |
| 656 |
> |
for (int i = 0; i < cgColData.position.size(); i++) |
| 657 |
> |
{ |
| 658 |
> |
cerr << "cgCpos = " << cgColData.position[i] << "\n"; |
| 659 |
> |
} |
| 660 |
> |
|
| 661 |
> |
// if needed, gather the atomic rotation matrices |
| 662 |
> |
if (storageLayout_ & DataStorage::dslAmat) |
| 663 |
> |
{ |
| 664 |
> |
AtomPlanMatrixRow->gather(snap_->atomData.aMat, |
| 665 |
> |
atomRowData.aMat); |
| 666 |
> |
AtomPlanMatrixColumn->gather(snap_->atomData.aMat, |
| 667 |
> |
atomColData.aMat); |
| 668 |
> |
} |
| 669 |
> |
|
| 670 |
> |
// if needed, gather the atomic eletrostatic frames |
| 671 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) |
| 672 |
> |
{ |
| 673 |
> |
AtomPlanMatrixRow->gather(snap_->atomData.electroFrame, |
| 674 |
> |
atomRowData.electroFrame); |
| 675 |
> |
AtomPlanMatrixColumn->gather(snap_->atomData.electroFrame, |
| 676 |
> |
atomColData.electroFrame); |
| 677 |
> |
} |
| 678 |
> |
|
| 679 |
> |
#endif |
| 680 |
> |
} |
| 681 |
> |
|
| 682 |
> |
/* collects information obtained during the pre-pair loop onto local |
| 683 |
> |
* data structures. |
| 684 |
> |
*/ |
| 685 |
> |
void ForceMatrixDecomposition::collectIntermediateData() { |
| 686 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 687 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 688 |
> |
#ifdef IS_MPI |
| 689 |
> |
|
| 690 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 691 |
> |
{ |
| 692 |
> |
|
| 693 |
> |
AtomPlanRealRow->scatter(atomRowData.density, |
| 694 |
> |
snap_->atomData.density); |
| 695 |
> |
|
| 696 |
> |
int n = snap_->atomData.density.size(); |
| 697 |
> |
vector<RealType> rho_tmp(n, 0.0); |
| 698 |
> |
AtomPlanRealColumn->scatter(atomColData.density, rho_tmp); |
| 699 |
> |
for (int i = 0; i < n; i++) |
| 700 |
> |
snap_->atomData.density[i] += rho_tmp[i]; |
| 701 |
> |
} |
| 702 |
> |
#endif |
| 703 |
> |
} |
| 704 |
> |
|
| 705 |
> |
/* |
| 706 |
> |
* redistributes information obtained during the pre-pair loop out to |
| 707 |
> |
* row and column-indexed data structures |
| 708 |
> |
*/ |
| 709 |
> |
void ForceMatrixDecomposition::distributeIntermediateData() { |
| 710 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 711 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 712 |
> |
#ifdef IS_MPI |
| 713 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 714 |
> |
{ |
| 715 |
> |
AtomPlanRealRow->gather(snap_->atomData.functional, |
| 716 |
> |
atomRowData.functional); |
| 717 |
> |
AtomPlanRealColumn->gather(snap_->atomData.functional, |
| 718 |
> |
atomColData.functional); |
| 719 |
> |
} |
| 720 |
> |
|
| 721 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 722 |
> |
{ |
| 723 |
> |
AtomPlanRealRow->gather(snap_->atomData.functionalDerivative, |
| 724 |
> |
atomRowData.functionalDerivative); |
| 725 |
> |
AtomPlanRealColumn->gather(snap_->atomData.functionalDerivative, |
| 726 |
> |
atomColData.functionalDerivative); |
| 727 |
> |
} |
| 728 |
> |
#endif |
| 729 |
> |
} |
| 730 |
> |
|
| 731 |
> |
void ForceMatrixDecomposition::collectData() { |
| 732 |
> |
snap_ = sman_->getCurrentSnapshot(); |
| 733 |
> |
storageLayout_ = sman_->getStorageLayout(); |
| 734 |
> |
#ifdef IS_MPI |
| 735 |
> |
int n = snap_->atomData.force.size(); |
| 736 |
> |
vector<Vector3d> frc_tmp(n, V3Zero); |
| 737 |
> |
|
| 738 |
> |
AtomPlanVectorRow->scatter(atomRowData.force, frc_tmp); |
| 739 |
> |
for (int i = 0; i < n; i++) |
| 740 |
> |
{ |
| 741 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 742 |
> |
frc_tmp[i] = 0.0; |
| 743 |
> |
} |
| 744 |
> |
|
| 745 |
> |
AtomPlanVectorColumn->scatter(atomColData.force, frc_tmp); |
| 746 |
> |
for (int i = 0; i < n; i++) |
| 747 |
> |
{ |
| 748 |
> |
snap_->atomData.force[i] += frc_tmp[i]; |
| 749 |
> |
} |
| 750 |
> |
|
| 751 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 752 |
> |
{ |
| 753 |
> |
|
| 754 |
> |
int nt = snap_->atomData.torque.size(); |
| 755 |
> |
vector<Vector3d> trq_tmp(nt, V3Zero); |
| 756 |
> |
|
| 757 |
> |
AtomPlanVectorRow->scatter(atomRowData.torque, trq_tmp); |
| 758 |
> |
for (int i = 0; i < nt; i++) |
| 759 |
> |
{ |
| 760 |
> |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 761 |
> |
trq_tmp[i] = 0.0; |
| 762 |
> |
} |
| 763 |
> |
|
| 764 |
> |
AtomPlanVectorColumn->scatter(atomColData.torque, trq_tmp); |
| 765 |
> |
for (int i = 0; i < nt; i++) |
| 766 |
> |
snap_->atomData.torque[i] += trq_tmp[i]; |
| 767 |
> |
} |
| 768 |
> |
|
| 769 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 770 |
> |
{ |
| 771 |
> |
|
| 772 |
> |
int ns = snap_->atomData.skippedCharge.size(); |
| 773 |
> |
vector<RealType> skch_tmp(ns, 0.0); |
| 774 |
> |
|
| 775 |
> |
AtomPlanRealRow->scatter(atomRowData.skippedCharge, skch_tmp); |
| 776 |
> |
for (int i = 0; i < ns; i++) |
| 777 |
> |
{ |
| 778 |
> |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 779 |
> |
skch_tmp[i] = 0.0; |
| 780 |
> |
} |
| 781 |
> |
|
| 782 |
> |
AtomPlanRealColumn->scatter(atomColData.skippedCharge, skch_tmp); |
| 783 |
> |
for (int i = 0; i < ns; i++) |
| 784 |
> |
snap_->atomData.skippedCharge[i] += skch_tmp[i]; |
| 785 |
> |
} |
| 786 |
> |
|
| 787 |
> |
nLocal_ = snap_->getNumberOfAtoms(); |
| 788 |
> |
|
| 789 |
> |
vector<potVec> pot_temp(nLocal_, |
| 790 |
> |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 791 |
> |
|
| 792 |
> |
// scatter/gather pot_row into the members of my column |
| 793 |
> |
|
| 794 |
> |
AtomPlanPotRow->scatter(pot_row, pot_temp); |
| 795 |
> |
|
| 796 |
> |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 797 |
> |
pairwisePot += pot_temp[ii]; |
| 798 |
> |
|
| 799 |
> |
fill(pot_temp.begin(), pot_temp.end(), |
| 800 |
> |
Vector<RealType, N_INTERACTION_FAMILIES> (0.0)); |
| 801 |
> |
|
| 802 |
> |
AtomPlanPotColumn->scatter(pot_col, pot_temp); |
| 803 |
> |
|
| 804 |
> |
for (int ii = 0; ii < pot_temp.size(); ii++ ) |
| 805 |
> |
pairwisePot += pot_temp[ii]; |
| 806 |
> |
#endif |
| 807 |
> |
|
| 808 |
> |
// cerr << "pairwisePot = " << pairwisePot << "\n"; |
| 809 |
> |
} |
| 810 |
> |
|
| 811 |
> |
int ForceMatrixDecomposition::getNAtomsInRow() { |
| 812 |
> |
#ifdef IS_MPI |
| 813 |
> |
return nAtomsInRow_; |
| 814 |
> |
#else |
| 815 |
> |
return nLocal_; |
| 816 |
> |
#endif |
| 817 |
> |
} |
| 818 |
> |
|
| 819 |
> |
/** |
| 820 |
> |
* returns the list of atoms belonging to this group. |
| 821 |
> |
*/ |
| 822 |
> |
vector<int> ForceMatrixDecomposition::getAtomsInGroupRow(int cg1) { |
| 823 |
> |
#ifdef IS_MPI |
| 824 |
> |
return groupListRow_[cg1]; |
| 825 |
> |
#else |
| 826 |
> |
return groupList_[cg1]; |
| 827 |
> |
#endif |
| 828 |
> |
} |
| 829 |
> |
|
| 830 |
> |
vector<int> ForceMatrixDecomposition::getAtomsInGroupColumn(int cg2) { |
| 831 |
> |
#ifdef IS_MPI |
| 832 |
> |
return groupListCol_[cg2]; |
| 833 |
> |
#else |
| 834 |
> |
return groupList_[cg2]; |
| 835 |
> |
#endif |
| 836 |
> |
} |
| 837 |
> |
|
| 838 |
> |
Vector3d ForceMatrixDecomposition::getIntergroupVector(int cg1, int cg2) { |
| 839 |
> |
Vector3d d; |
| 840 |
> |
|
| 841 |
> |
#ifdef IS_MPI |
| 842 |
> |
d = cgColData.position[cg2] - cgRowData.position[cg1]; |
| 843 |
> |
cerr << "cg1 = " << cg1 << "\tcg1p = " << cgRowData.position[cg1] << "\n"; |
| 844 |
> |
cerr << "cg2 = " << cg2 << "\tcg2p = " << cgColData.position[cg2] << "\n"; |
| 845 |
> |
#else |
| 846 |
> |
d = snap_->cgData.position[cg2] - snap_->cgData.position[cg1]; |
| 847 |
> |
cerr << "cg1 = " << cg1 << "\tcg1p = " << snap_->cgData.position[cg1] << "\n"; |
| 848 |
> |
cerr << "cg2 = " << cg2 << "\tcg2p = " << snap_->cgData.position[cg2] << "\n"; |
| 849 |
> |
#endif |
| 850 |
> |
|
| 851 |
> |
snap_->wrapVector(d); |
| 852 |
> |
return d; |
| 853 |
> |
} |
| 854 |
> |
|
| 855 |
> |
Vector3d ForceMatrixDecomposition::getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2) { |
| 856 |
> |
Vector3d d; |
| 857 |
> |
|
| 858 |
> |
d = snap_->cgData.position[cg2->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()]; |
| 859 |
> |
/* cerr << "cg1_gid = " << cg1->getGlobalIndex() << "\tcg1_lid = " << cg1->getLocalIndex() << "\tcg1p = " |
| 860 |
> |
<< snap_->cgData.position[cg1->getLocalIndex()] << "\n"; |
| 861 |
> |
cerr << "cg2_gid = " << cg2->getGlobalIndex() << "\tcg2_lid = " << cg2->getLocalIndex() << "\tcg2p = " |
| 862 |
> |
<< snap_->cgData.position[cg2->getLocalIndex()] << "\n";*/ |
| 863 |
> |
|
| 864 |
> |
snap_->wrapVector(d); |
| 865 |
> |
return d; |
| 866 |
> |
} |
| 867 |
> |
|
| 868 |
> |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorRow(int atom1, int cg1) { |
| 869 |
> |
|
| 870 |
> |
Vector3d d; |
| 871 |
> |
|
| 872 |
> |
#ifdef IS_MPI |
| 873 |
> |
d = cgRowData.position[cg1] - atomRowData.position[atom1]; |
| 874 |
> |
#else |
| 875 |
> |
d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; |
| 876 |
> |
#endif |
| 877 |
> |
|
| 878 |
> |
snap_->wrapVector(d); |
| 879 |
> |
return d; |
| 880 |
> |
} |
| 881 |
> |
|
| 882 |
> |
Vector3d ForceMatrixDecomposition::getAtomToGroupVectorColumn(int atom2, int cg2) { |
| 883 |
> |
Vector3d d; |
| 884 |
> |
|
| 885 |
> |
#ifdef IS_MPI |
| 886 |
> |
d = cgColData.position[cg2] - atomColData.position[atom2]; |
| 887 |
> |
#else |
| 888 |
> |
d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; |
| 889 |
> |
#endif |
| 890 |
> |
|
| 891 |
> |
snap_->wrapVector(d); |
| 892 |
> |
return d; |
| 893 |
> |
} |
| 894 |
> |
|
| 895 |
> |
RealType ForceMatrixDecomposition::getMassFactorRow(int atom1) { |
| 896 |
> |
#ifdef IS_MPI |
| 897 |
> |
return massFactorsRow[atom1]; |
| 898 |
> |
#else |
| 899 |
> |
return massFactors[atom1]; |
| 900 |
> |
#endif |
| 901 |
> |
} |
| 902 |
> |
|
| 903 |
> |
RealType ForceMatrixDecomposition::getMassFactorColumn(int atom2) { |
| 904 |
> |
#ifdef IS_MPI |
| 905 |
> |
return massFactorsCol[atom2]; |
| 906 |
> |
#else |
| 907 |
> |
return massFactors[atom2]; |
| 908 |
> |
#endif |
| 909 |
> |
|
| 910 |
> |
} |
| 911 |
> |
|
| 912 |
> |
Vector3d ForceMatrixDecomposition::getInteratomicVector(int atom1, int atom2) { |
| 913 |
> |
Vector3d d; |
| 914 |
> |
|
| 915 |
> |
#ifdef IS_MPI |
| 916 |
> |
d = atomColData.position[atom2] - atomRowData.position[atom1]; |
| 917 |
> |
#else |
| 918 |
> |
d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; |
| 919 |
> |
#endif |
| 920 |
> |
|
| 921 |
> |
snap_->wrapVector(d); |
| 922 |
> |
return d; |
| 923 |
> |
} |
| 924 |
> |
|
| 925 |
> |
vector<int> ForceMatrixDecomposition::getExcludesForAtom(int atom1) { |
| 926 |
> |
return excludesForAtom[atom1]; |
| 927 |
> |
} |
| 928 |
> |
|
| 929 |
> |
/** |
| 930 |
> |
* We need to exclude some overcounted interactions that result from |
| 931 |
> |
* the parallel decomposition. |
| 932 |
> |
*/ |
| 933 |
> |
bool ForceMatrixDecomposition::skipAtomPair(int atom1, int atom2) { |
| 934 |
> |
int unique_id_1, unique_id_2; |
| 935 |
> |
|
| 936 |
> |
// cerr << "sap with atom1, atom2 =\t" << atom1 << "\t" << atom2 << "\n"; |
| 937 |
> |
#ifdef IS_MPI |
| 938 |
> |
// in MPI, we have to look up the unique IDs for each atom |
| 939 |
> |
unique_id_1 = AtomRowToGlobal[atom1]; |
| 940 |
> |
unique_id_2 = AtomColToGlobal[atom2]; |
| 941 |
> |
|
| 942 |
> |
cerr << "sap with uid1, uid2 =\t" << unique_id_1 << "\t" << unique_id_2 << "\n"; |
| 943 |
> |
// this situation should only arise in MPI simulations |
| 944 |
> |
if (unique_id_1 == unique_id_2) return true; |
| 945 |
> |
|
| 946 |
> |
// this prevents us from doing the pair on multiple processors |
| 947 |
> |
if (unique_id_1 < unique_id_2) |
| 948 |
> |
{ |
| 949 |
> |
if ((unique_id_1 + unique_id_2) % 2 == 0) return true; |
| 950 |
> |
} else |
| 951 |
> |
{ |
| 952 |
> |
if ((unique_id_1 + unique_id_2) % 2 == 1) return true; |
| 953 |
> |
} |
| 954 |
> |
#endif |
| 955 |
> |
return false; |
| 956 |
> |
} |
| 957 |
> |
|
| 958 |
> |
/** |
| 959 |
> |
* We need to handle the interactions for atoms who are involved in |
| 960 |
> |
* the same rigid body as well as some short range interactions |
| 961 |
> |
* (bonds, bends, torsions) differently from other interactions. |
| 962 |
> |
* We'll still visit the pairwise routines, but with a flag that |
| 963 |
> |
* tells those routines to exclude the pair from direct long range |
| 964 |
> |
* interactions. Some indirect interactions (notably reaction |
| 965 |
> |
* field) must still be handled for these pairs. |
| 966 |
> |
*/ |
| 967 |
> |
bool ForceMatrixDecomposition::excludeAtomPair(int atom1, int atom2) { |
| 968 |
> |
int unique_id_2; |
| 969 |
> |
#ifdef IS_MPI |
| 970 |
> |
// in MPI, we have to look up the unique IDs for the row atom. |
| 971 |
> |
unique_id_2 = AtomColToGlobal[atom2]; |
| 972 |
> |
#else |
| 973 |
> |
// in the normal loop, the atom numbers are unique |
| 974 |
> |
unique_id_2 = atom2; |
| 975 |
> |
#endif |
| 976 |
> |
|
| 977 |
> |
for (vector<int>::iterator i = excludesForAtom[atom1].begin(); i != excludesForAtom[atom1].end(); ++i) |
| 978 |
> |
{ |
| 979 |
> |
if ((*i) == unique_id_2) |
| 980 |
> |
return true; |
| 981 |
> |
} |
| 982 |
> |
|
| 983 |
> |
return false; |
| 984 |
> |
} |
| 985 |
> |
|
| 986 |
> |
void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg) { |
| 987 |
> |
#ifdef IS_MPI |
| 988 |
> |
atomRowData.force[atom1] += fg; |
| 989 |
> |
#else |
| 990 |
> |
snap_->atomData.force[atom1] += fg; |
| 991 |
> |
#endif |
| 992 |
> |
} |
| 993 |
> |
|
| 994 |
> |
void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg) { |
| 995 |
> |
#ifdef IS_MPI |
| 996 |
> |
atomColData.force[atom2] += fg; |
| 997 |
> |
#else |
| 998 |
> |
snap_->atomData.force[atom2] += fg; |
| 999 |
> |
#endif |
| 1000 |
> |
} |
| 1001 |
> |
|
| 1002 |
> |
// filling interaction blocks with pointers |
| 1003 |
> |
void ForceMatrixDecomposition::fillInteractionData(InteractionData &idat, int atom1, int atom2) { |
| 1004 |
> |
|
| 1005 |
> |
idat.excluded = excludeAtomPair(atom1, atom2); |
| 1006 |
> |
|
| 1007 |
> |
#ifdef IS_MPI |
| 1008 |
> |
idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
| 1009 |
> |
//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 1010 |
> |
// ff_->getAtomType(identsCol[atom2]) ); |
| 1011 |
> |
|
| 1012 |
> |
if (storageLayout_ & DataStorage::dslAmat) |
| 1013 |
> |
{ |
| 1014 |
> |
idat.A1 = &(atomRowData.aMat[atom1]); |
| 1015 |
> |
idat.A2 = &(atomColData.aMat[atom2]); |
| 1016 |
> |
} |
| 1017 |
> |
|
| 1018 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) |
| 1019 |
> |
{ |
| 1020 |
> |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 1021 |
> |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 1022 |
> |
} |
| 1023 |
> |
|
| 1024 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 1025 |
> |
{ |
| 1026 |
> |
idat.t1 = &(atomRowData.torque[atom1]); |
| 1027 |
> |
idat.t2 = &(atomColData.torque[atom2]); |
| 1028 |
> |
} |
| 1029 |
> |
|
| 1030 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 1031 |
> |
{ |
| 1032 |
> |
idat.rho1 = &(atomRowData.density[atom1]); |
| 1033 |
> |
idat.rho2 = &(atomColData.density[atom2]); |
| 1034 |
> |
} |
| 1035 |
> |
|
| 1036 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 1037 |
> |
{ |
| 1038 |
> |
idat.frho1 = &(atomRowData.functional[atom1]); |
| 1039 |
> |
idat.frho2 = &(atomColData.functional[atom2]); |
| 1040 |
> |
} |
| 1041 |
> |
|
| 1042 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 1043 |
> |
{ |
| 1044 |
> |
idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 1045 |
> |
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 1046 |
> |
} |
| 1047 |
> |
|
| 1048 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 1049 |
> |
{ |
| 1050 |
> |
idat.particlePot1 = &(atomRowData.particlePot[atom1]); |
| 1051 |
> |
idat.particlePot2 = &(atomColData.particlePot[atom2]); |
| 1052 |
> |
} |
| 1053 |
> |
|
| 1054 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 1055 |
> |
{ |
| 1056 |
> |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 1057 |
> |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 1058 |
> |
} |
| 1059 |
> |
|
| 1060 |
> |
#else |
| 1061 |
> |
|
| 1062 |
> |
idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]); |
| 1063 |
> |
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 1064 |
> |
// ff_->getAtomType(idents[atom2]) ); |
| 1065 |
> |
|
| 1066 |
> |
if (storageLayout_ & DataStorage::dslAmat) |
| 1067 |
> |
{ |
| 1068 |
> |
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 1069 |
> |
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 1070 |
> |
} |
| 1071 |
> |
|
| 1072 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) |
| 1073 |
> |
{ |
| 1074 |
> |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 1075 |
> |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 1076 |
> |
} |
| 1077 |
> |
|
| 1078 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 1079 |
> |
{ |
| 1080 |
> |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 1081 |
> |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 1082 |
> |
} |
| 1083 |
> |
|
| 1084 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 1085 |
> |
{ |
| 1086 |
> |
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 1087 |
> |
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 1088 |
> |
} |
| 1089 |
> |
|
| 1090 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 1091 |
> |
{ |
| 1092 |
> |
idat.frho1 = &(snap_->atomData.functional[atom1]); |
| 1093 |
> |
idat.frho2 = &(snap_->atomData.functional[atom2]); |
| 1094 |
> |
} |
| 1095 |
> |
|
| 1096 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 1097 |
> |
{ |
| 1098 |
> |
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 1099 |
> |
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 1100 |
> |
} |
| 1101 |
> |
|
| 1102 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 1103 |
> |
{ |
| 1104 |
> |
idat.particlePot1 = &(snap_->atomData.particlePot[atom1]); |
| 1105 |
> |
idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
| 1106 |
> |
} |
| 1107 |
> |
|
| 1108 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 1109 |
> |
{ |
| 1110 |
> |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 1111 |
> |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 1112 |
> |
} |
| 1113 |
> |
#endif |
| 1114 |
> |
} |
| 1115 |
> |
|
| 1116 |
> |
// filling interaction blocks with pointers |
| 1117 |
> |
void ForceMatrixDecomposition::fillInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) { |
| 1118 |
> |
|
| 1119 |
> |
idat.excluded = excludeAtomPair(atom1, atom2); |
| 1120 |
> |
|
| 1121 |
> |
#ifdef IS_MPI |
| 1122 |
> |
idat.atypes = make_pair( atypesRow[atom1], atypesCol[atom2]); |
| 1123 |
> |
//idat.atypes = make_pair( ff_->getAtomType(identsRow[atom1]), |
| 1124 |
> |
// ff_->getAtomType(identsCol[atom2]) ); |
| 1125 |
> |
|
| 1126 |
> |
if (storageLayout_ & DataStorage::dslAmat) |
| 1127 |
> |
{ |
| 1128 |
> |
idat.A1 = &(atomRowData.aMat[atom1]); |
| 1129 |
> |
idat.A2 = &(atomColData.aMat[atom2]); |
| 1130 |
> |
} |
| 1131 |
> |
|
| 1132 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) |
| 1133 |
> |
{ |
| 1134 |
> |
idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 1135 |
> |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
| 1136 |
> |
} |
| 1137 |
> |
|
| 1138 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 1139 |
> |
{ |
| 1140 |
> |
idat.t1 = &(atomRowData.torque[atom1]); |
| 1141 |
> |
idat.t2 = &(atomColData.torque[atom2]); |
| 1142 |
> |
} |
| 1143 |
> |
|
| 1144 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 1145 |
> |
{ |
| 1146 |
> |
idat.rho1 = &(atomRowData.density[atom1]); |
| 1147 |
> |
idat.rho2 = &(atomColData.density[atom2]); |
| 1148 |
> |
} |
| 1149 |
> |
|
| 1150 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 1151 |
> |
{ |
| 1152 |
> |
idat.frho1 = &(atomRowData.functional[atom1]); |
| 1153 |
> |
idat.frho2 = &(atomColData.functional[atom2]); |
| 1154 |
> |
} |
| 1155 |
> |
|
| 1156 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 1157 |
> |
{ |
| 1158 |
> |
idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
| 1159 |
> |
idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
| 1160 |
> |
} |
| 1161 |
> |
|
| 1162 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 1163 |
> |
{ |
| 1164 |
> |
idat.particlePot1 = &(atomRowData.particlePot[atom1]); |
| 1165 |
> |
idat.particlePot2 = &(atomColData.particlePot[atom2]); |
| 1166 |
> |
} |
| 1167 |
> |
|
| 1168 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 1169 |
> |
{ |
| 1170 |
> |
idat.skippedCharge1 = &(atomRowData.skippedCharge[atom1]); |
| 1171 |
> |
idat.skippedCharge2 = &(atomColData.skippedCharge[atom2]); |
| 1172 |
> |
} |
| 1173 |
> |
|
| 1174 |
> |
#else |
| 1175 |
> |
|
| 1176 |
> |
idat.atypes = make_pair(atypesLocal[atom1], atypesLocal[atom2]); |
| 1177 |
> |
//idat.atypes = make_pair( ff_->getAtomType(idents[atom1]), |
| 1178 |
> |
// ff_->getAtomType(idents[atom2]) ); |
| 1179 |
> |
|
| 1180 |
> |
if (storageLayout_ & DataStorage::dslAmat) |
| 1181 |
> |
{ |
| 1182 |
> |
idat.A1 = &(snap_->atomData.aMat[atom1]); |
| 1183 |
> |
idat.A2 = &(snap_->atomData.aMat[atom2]); |
| 1184 |
> |
} |
| 1185 |
> |
|
| 1186 |
> |
if (storageLayout_ & DataStorage::dslElectroFrame) |
| 1187 |
> |
{ |
| 1188 |
> |
idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 1189 |
> |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 1190 |
> |
} |
| 1191 |
> |
|
| 1192 |
> |
if (storageLayout_ & DataStorage::dslTorque) |
| 1193 |
> |
{ |
| 1194 |
> |
idat.t1 = &(snap_->atomData.torque[atom1]); |
| 1195 |
> |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 1196 |
> |
} |
| 1197 |
> |
|
| 1198 |
> |
if (storageLayout_ & DataStorage::dslDensity) |
| 1199 |
> |
{ |
| 1200 |
> |
idat.rho1 = &(snap_->atomData.density[atom1]); |
| 1201 |
> |
idat.rho2 = &(snap_->atomData.density[atom2]); |
| 1202 |
> |
} |
| 1203 |
> |
|
| 1204 |
> |
if (storageLayout_ & DataStorage::dslFunctional) |
| 1205 |
> |
{ |
| 1206 |
> |
idat.frho1 = &(snap_->atomData.functional[atom1]); |
| 1207 |
> |
idat.frho2 = &(snap_->atomData.functional[atom2]); |
| 1208 |
> |
} |
| 1209 |
> |
|
| 1210 |
> |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) |
| 1211 |
> |
{ |
| 1212 |
> |
idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
| 1213 |
> |
idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
| 1214 |
> |
} |
| 1215 |
> |
|
| 1216 |
> |
if (storageLayout_ & DataStorage::dslParticlePot) |
| 1217 |
> |
{ |
| 1218 |
> |
idat.particlePot1 = &(snap_->atomData.particlePot[atom1]); |
| 1219 |
> |
idat.particlePot2 = &(snap_->atomData.particlePot[atom2]); |
| 1220 |
> |
} |
| 1221 |
> |
|
| 1222 |
> |
if (storageLayout_ & DataStorage::dslSkippedCharge) |
| 1223 |
> |
{ |
| 1224 |
> |
idat.skippedCharge1 = &(snap_->atomData.skippedCharge[atom1]); |
| 1225 |
> |
idat.skippedCharge2 = &(snap_->atomData.skippedCharge[atom2]); |
| 1226 |
> |
} |
| 1227 |
> |
#endif |
| 1228 |
> |
} |
| 1229 |
> |
|
| 1230 |
> |
void ForceMatrixDecomposition::unpackInteractionData(InteractionData &idat, int atom1, int atom2) { |
| 1231 |
> |
#ifdef IS_MPI |
| 1232 |
> |
pot_row[atom1] += 0.5 * *(idat.pot); |
| 1233 |
> |
pot_col[atom2] += 0.5 * *(idat.pot); |
| 1234 |
> |
|
| 1235 |
> |
atomRowData.force[atom1] += *(idat.f1); |
| 1236 |
> |
atomColData.force[atom2] -= *(idat.f1); |
| 1237 |
> |
#else |
| 1238 |
> |
pairwisePot += *(idat.pot); |
| 1239 |
> |
|
| 1240 |
> |
snap_->atomData.force[atom1] += *(idat.f1); |
| 1241 |
> |
snap_->atomData.force[atom2] -= *(idat.f1); |
| 1242 |
> |
#endif |
| 1243 |
> |
|
| 1244 |
> |
} |
| 1245 |
> |
|
| 1246 |
> |
void ForceMatrixDecomposition::unpackInteractionDataOMP(InteractionDataPrv &idat, int atom1, int atom2) { |
| 1247 |
> |
pairwisePot += idat.pot; |
| 1248 |
> |
|
| 1249 |
> |
snap_->atomData.force[atom1] += idat.f1; |
| 1250 |
> |
snap_->atomData.force[atom2] -= idat.f1; |
| 1251 |
> |
} |
| 1252 |
> |
|
| 1253 |
> |
void ForceMatrixDecomposition::reorderGroupCutoffs(vector<int> &order) { |
| 1254 |
> |
vector<int> tmp = vector<int> (groupToGtype.size()); |
| 1255 |
> |
|
| 1256 |
> |
for (int i = 0; i < groupToGtype.size(); ++i) |
| 1257 |
> |
{ |
| 1258 |
> |
tmp[i] = groupToGtype[i]; |
| 1259 |
> |
} |
| 1260 |
> |
|
| 1261 |
> |
for (int i = 0; i < groupToGtype.size(); ++i) |
| 1262 |
> |
{ |
| 1263 |
> |
groupToGtype[i] = tmp[order[i]]; |
| 1264 |
> |
} |
| 1265 |
> |
} |
| 1266 |
> |
|
| 1267 |
> |
void ForceMatrixDecomposition::reorderPosition(vector<int> &order) { |
| 1268 |
> |
Snapshot* snap_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 1269 |
> |
DataStorage* cgConfig = &(snap_->cgData); |
| 1270 |
> |
vector<Vector3d> tmp = vector<Vector3d> (nGroups_); |
| 1271 |
> |
|
| 1272 |
> |
for (int i = 0; i < nGroups_; ++i) |
| 1273 |
> |
{ |
| 1274 |
> |
tmp[i] = snap_->cgData.position[i]; |
| 1275 |
> |
} |
| 1276 |
> |
|
| 1277 |
> |
vector<int> mapPos = vector<int> (nGroups_); |
| 1278 |
> |
for (int i = 0; i < nGroups_; ++i) |
| 1279 |
> |
{ |
| 1280 |
> |
snap_->cgData.position[i] = tmp[order[i]]; |
| 1281 |
> |
mapPos[order[i]] = i; |
| 1282 |
> |
} |
| 1283 |
> |
|
| 1284 |
> |
SimInfo::MoleculeIterator mi; |
| 1285 |
> |
Molecule* mol; |
| 1286 |
> |
Molecule::CutoffGroupIterator ci; |
| 1287 |
> |
CutoffGroup* cg; |
| 1288 |
> |
|
| 1289 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) |
| 1290 |
> |
{ |
| 1291 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) |
| 1292 |
> |
{ |
| 1293 |
> |
cg->setLocalIndex(mapPos[cg->getLocalIndex()]); |
| 1294 |
> |
} |
| 1295 |
> |
} |
| 1296 |
> |
} |
| 1297 |
> |
|
| 1298 |
> |
void ForceMatrixDecomposition::reorderGroupList(vector<int> &order) { |
| 1299 |
> |
vector<vector<int> > tmp = vector<vector<int> > (groupList_.size()); |
| 1300 |
> |
|
| 1301 |
> |
for (int i = 0; i < groupList_.size(); ++i) |
| 1302 |
> |
{ |
| 1303 |
> |
tmp[i] = groupList_[i]; |
| 1304 |
> |
} |
| 1305 |
> |
|
| 1306 |
> |
for (int i = 0; i < groupList_.size(); ++i) |
| 1307 |
> |
{ |
| 1308 |
> |
groupList_[i] = tmp[order[i]]; |
| 1309 |
> |
} |
| 1310 |
> |
} |
| 1311 |
> |
|
| 1312 |
> |
void ForceMatrixDecomposition::reorderMemory(vector<vector<CutoffGroup *> > &H_c_l) { |
| 1313 |
> |
int n = 0; |
| 1314 |
> |
|
| 1315 |
> |
/* record the reordered atom indices */ |
| 1316 |
> |
vector<int> k = vector<int> (nGroups_); |
| 1317 |
> |
|
| 1318 |
> |
for (int c = 0; c < H_c_l.size(); ++c) |
| 1319 |
> |
{ |
| 1320 |
> |
for (vector<CutoffGroup *>::iterator cg = H_c_l[c].begin(); cg != H_c_l[c].end(); ++cg) |
| 1321 |
> |
{ |
| 1322 |
> |
int i = (*cg)->getGlobalIndex(); |
| 1323 |
> |
k[n] = i; |
| 1324 |
> |
++n; |
| 1325 |
> |
} |
| 1326 |
> |
} |
| 1327 |
> |
|
| 1328 |
> |
// reorderGroupCutoffs(k); |
| 1329 |
> |
// reorderGroupList(k); |
| 1330 |
> |
reorderPosition(k); |
| 1331 |
> |
} |
| 1332 |
> |
|
| 1333 |
> |
vector<vector<CutoffGroup *> > ForceMatrixDecomposition::buildLayerBasedNeighborList() { |
| 1334 |
> |
// Na = nGroups_ |
| 1335 |
> |
/* cell occupancy counter */ |
| 1336 |
> |
// vector<int> k_c; |
| 1337 |
> |
/* c_i - has cell containing atom i (size Na) */ |
| 1338 |
> |
vector<int> c = vector<int> (nGroups_); |
| 1339 |
> |
/* l_i - layer containing atom i (size Na) */ |
| 1340 |
> |
// vector<int> l; |
| 1341 |
> |
|
| 1342 |
> |
RealType rList_ = (largestRcut_ + skinThickness_); |
| 1343 |
> |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 1344 |
> |
Mat3x3d Hmat = snap_->getHmat(); |
| 1345 |
> |
Vector3d Hx = Hmat.getColumn(0); |
| 1346 |
> |
Vector3d Hy = Hmat.getColumn(1); |
| 1347 |
> |
Vector3d Hz = Hmat.getColumn(2); |
| 1348 |
> |
|
| 1349 |
> |
nCells_.x() = (int) (Hx.length()) / rList_; |
| 1350 |
> |
nCells_.y() = (int) (Hy.length()) / rList_; |
| 1351 |
> |
nCells_.z() = (int) (Hz.length()) / rList_; |
| 1352 |
> |
|
| 1353 |
> |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 1354 |
> |
Vector3d rs, scaled, dr; |
| 1355 |
> |
Vector3i whichCell; |
| 1356 |
> |
int cellIndex; |
| 1357 |
> |
int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
| 1358 |
> |
|
| 1359 |
> |
// k_c = vector<int> (nCtot, 0); |
| 1360 |
> |
|
| 1361 |
> |
SimInfo::MoleculeIterator mi; |
| 1362 |
> |
Molecule* mol; |
| 1363 |
> |
Molecule::CutoffGroupIterator ci; |
| 1364 |
> |
CutoffGroup* cg; |
| 1365 |
> |
|
| 1366 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) |
| 1367 |
> |
{ |
| 1368 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) |
| 1369 |
> |
{ |
| 1370 |
> |
rs = snap_->cgData.position[cg->getLocalIndex()]; |
| 1371 |
> |
|
| 1372 |
> |
// scaled positions relative to the box vectors |
| 1373 |
> |
scaled = invHmat * rs; |
| 1374 |
> |
|
| 1375 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1376 |
> |
// numbers |
| 1377 |
> |
for (int j = 0; j < 3; j++) |
| 1378 |
> |
{ |
| 1379 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1380 |
> |
scaled[j] += 0.5; |
| 1381 |
> |
} |
| 1382 |
> |
|
| 1383 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1384 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1385 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1386 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1387 |
> |
|
| 1388 |
> |
// printf("pos x:%f y:%f z:%f cell x:%d y:%d z:%d\n", rs.x(), rs.y(), rs.z(), whichCell.x(), whichCell.y(), |
| 1389 |
> |
// whichCell.z()); |
| 1390 |
> |
|
| 1391 |
> |
// find single index of this cell: |
| 1392 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1393 |
> |
|
| 1394 |
> |
c[cg->getGlobalIndex()] = cellIndex; |
| 1395 |
> |
} |
| 1396 |
> |
} |
| 1397 |
> |
|
| 1398 |
> |
// int k_c_curr; |
| 1399 |
> |
// int k_c_max = 0; |
| 1400 |
> |
/* the cell-layer occupancy matrix */ |
| 1401 |
> |
vector<vector<CutoffGroup *> > H_c_l = vector<vector<CutoffGroup *> > (nCtot); |
| 1402 |
> |
|
| 1403 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) |
| 1404 |
> |
{ |
| 1405 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) |
| 1406 |
> |
|
| 1407 |
> |
{ |
| 1408 |
> |
// k_c_curr = ++k_c[c[cg1->getGlobalIndex()]]; |
| 1409 |
> |
// l.push_back(k_c_curr); |
| 1410 |
> |
// |
| 1411 |
> |
// /* determines the number of layers in use */ |
| 1412 |
> |
// if (k_c_max < k_c_curr) |
| 1413 |
> |
// { |
| 1414 |
> |
// k_c_max = k_c_curr; |
| 1415 |
> |
// } |
| 1416 |
> |
H_c_l[c[cg->getGlobalIndex()]].push_back(/*l[*/cg/*]*/); |
| 1417 |
> |
} |
| 1418 |
> |
} |
| 1419 |
> |
|
| 1420 |
> |
/* Frequency of reordering the memory */ |
| 1421 |
> |
if (neighborListReorderFreq != 0) |
| 1422 |
> |
{ |
| 1423 |
> |
if (reorderFreqCounter == neighborListReorderFreq) |
| 1424 |
> |
{ |
| 1425 |
> |
reorderMemory(H_c_l); |
| 1426 |
> |
reorderFreqCounter = 1; |
| 1427 |
> |
} else |
| 1428 |
> |
{ |
| 1429 |
> |
reorderFreqCounter++; |
| 1430 |
> |
} |
| 1431 |
> |
} |
| 1432 |
> |
|
| 1433 |
> |
int m; |
| 1434 |
> |
/* The neighbor matrix */ |
| 1435 |
> |
vector<vector<CutoffGroup *> > neighborMatW = vector<vector<CutoffGroup *> > (nGroups_); |
| 1436 |
> |
|
| 1437 |
> |
groupCutoffs cuts; |
| 1438 |
> |
CutoffGroup *cg1; |
| 1439 |
> |
|
| 1440 |
> |
/* Loops over objects(atoms, rigidBodies, cutoffGroups, etc.) */ |
| 1441 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) |
| 1442 |
> |
{ |
| 1443 |
> |
for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci)) |
| 1444 |
> |
{ |
| 1445 |
> |
/* c' */ |
| 1446 |
> |
int c1 = c[cg1->getGlobalIndex()]; |
| 1447 |
> |
Vector3i c1v = idxToV(c1, nCells_); |
| 1448 |
> |
|
| 1449 |
> |
/* loops over the neighboring cells c'' */ |
| 1450 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os) |
| 1451 |
> |
{ |
| 1452 |
> |
Vector3i c2v = c1v + (*os); |
| 1453 |
> |
|
| 1454 |
> |
if (c2v.x() >= nCells_.x()) |
| 1455 |
> |
{ |
| 1456 |
> |
c2v.x() = 0; |
| 1457 |
> |
} else if (c2v.x() < 0) |
| 1458 |
> |
{ |
| 1459 |
> |
c2v.x() = nCells_.x() - 1; |
| 1460 |
> |
} |
| 1461 |
> |
|
| 1462 |
> |
if (c2v.y() >= nCells_.y()) |
| 1463 |
> |
{ |
| 1464 |
> |
c2v.y() = 0; |
| 1465 |
> |
} else if (c2v.y() < 0) |
| 1466 |
> |
{ |
| 1467 |
> |
c2v.y() = nCells_.y() - 1; |
| 1468 |
> |
} |
| 1469 |
> |
|
| 1470 |
> |
if (c2v.z() >= nCells_.z()) |
| 1471 |
> |
{ |
| 1472 |
> |
c2v.z() = 0; |
| 1473 |
> |
} else if (c2v.z() < 0) |
| 1474 |
> |
{ |
| 1475 |
> |
c2v.z() = nCells_.z() - 1; |
| 1476 |
> |
} |
| 1477 |
> |
|
| 1478 |
> |
int c2 = Vlinear(c2v, nCells_); |
| 1479 |
> |
/* Loops over layers l to access the neighbor atoms */ |
| 1480 |
> |
for (vector<CutoffGroup *>::iterator cg2 = H_c_l[c2].begin(); cg2 != H_c_l[c2].end(); ++cg2) |
| 1481 |
> |
{ |
| 1482 |
> |
// if i'' = 0 then break // doesn't apply to vector implementation of the matrix |
| 1483 |
> |
// if(i != *j) |
| 1484 |
> |
if (c2 != c1 || (*cg2)->getGlobalIndex() < cg1->getGlobalIndex()) |
| 1485 |
> |
{ |
| 1486 |
> |
dr = snap_->cgData.position[(*cg2)->getLocalIndex()] - snap_->cgData.position[cg1->getLocalIndex()]; |
| 1487 |
> |
snap_->wrapVector(dr); |
| 1488 |
> |
cuts = getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex()); |
| 1489 |
> |
if (dr.lengthSquare() < cuts.third) |
| 1490 |
> |
{ |
| 1491 |
> |
/* Transposed version of Rapaport W mat, to occupy successive memory locations on CPU */ |
| 1492 |
> |
neighborMatW[cg1->getGlobalIndex()].push_back((*cg2)); |
| 1493 |
> |
} |
| 1494 |
> |
} |
| 1495 |
> |
} |
| 1496 |
> |
} |
| 1497 |
> |
} |
| 1498 |
> |
} |
| 1499 |
> |
|
| 1500 |
> |
// save the local cutoff group positions for the check that is |
| 1501 |
> |
// done on each loop: |
| 1502 |
> |
saved_CG_positions_.clear(); |
| 1503 |
> |
for (int i = 0; i < nGroups_; i++) |
| 1504 |
> |
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 1505 |
> |
|
| 1506 |
> |
return neighborMatW; |
| 1507 |
> |
} |
| 1508 |
> |
|
| 1509 |
> |
/* |
| 1510 |
> |
* buildNeighborList |
| 1511 |
> |
* |
| 1512 |
> |
* first element of pair is row-indexed CutoffGroup |
| 1513 |
> |
* second element of pair is column-indexed CutoffGroup |
| 1514 |
> |
*/ |
| 1515 |
> |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 1516 |
> |
|
| 1517 |
> |
vector<pair<int, int> > neighborList; |
| 1518 |
> |
groupCutoffs cuts; |
| 1519 |
> |
bool doAllPairs = false; |
| 1520 |
> |
|
| 1521 |
> |
#ifdef IS_MPI |
| 1522 |
> |
cellListRow_.clear(); |
| 1523 |
> |
cellListCol_.clear(); |
| 1524 |
> |
#else |
| 1525 |
> |
cellList_.clear(); |
| 1526 |
> |
#endif |
| 1527 |
> |
|
| 1528 |
> |
RealType rList_ = (largestRcut_ + skinThickness_); |
| 1529 |
> |
RealType rl2 = rList_ * rList_; |
| 1530 |
> |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 1531 |
> |
Mat3x3d Hmat = snap_->getHmat(); |
| 1532 |
> |
Vector3d Hx = Hmat.getColumn(0); |
| 1533 |
> |
Vector3d Hy = Hmat.getColumn(1); |
| 1534 |
> |
Vector3d Hz = Hmat.getColumn(2); |
| 1535 |
> |
|
| 1536 |
> |
nCells_.x() = (int) (Hx.length()) / rList_; |
| 1537 |
> |
nCells_.y() = (int) (Hy.length()) / rList_; |
| 1538 |
> |
nCells_.z() = (int) (Hz.length()) / rList_; |
| 1539 |
> |
|
| 1540 |
> |
// handle small boxes where the cell offsets can end up repeating cells |
| 1541 |
> |
|
| 1542 |
> |
if (nCells_.x() < 3) |
| 1543 |
> |
doAllPairs = true; |
| 1544 |
> |
if (nCells_.y() < 3) |
| 1545 |
> |
doAllPairs = true; |
| 1546 |
> |
if (nCells_.z() < 3) |
| 1547 |
> |
doAllPairs = true; |
| 1548 |
> |
|
| 1549 |
> |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 1550 |
> |
Vector3d rs, scaled, dr; |
| 1551 |
> |
Vector3i whichCell; |
| 1552 |
> |
int cellIndex; |
| 1553 |
> |
int nCtot = nCells_.x() * nCells_.y() * nCells_.z(); |
| 1554 |
> |
|
| 1555 |
> |
#ifdef IS_MPI |
| 1556 |
> |
cellListRow_.resize(nCtot); |
| 1557 |
> |
cellListCol_.resize(nCtot); |
| 1558 |
> |
#else |
| 1559 |
> |
cellList_.resize(nCtot); |
| 1560 |
> |
#endif |
| 1561 |
> |
|
| 1562 |
> |
if (!doAllPairs) |
| 1563 |
> |
{ |
| 1564 |
> |
#ifdef IS_MPI |
| 1565 |
> |
|
| 1566 |
> |
for (int i = 0; i < nGroupsInRow_; i++) |
| 1567 |
> |
{ |
| 1568 |
> |
rs = cgRowData.position[i]; |
| 1569 |
> |
|
| 1570 |
> |
// scaled positions relative to the box vectors |
| 1571 |
> |
scaled = invHmat * rs; |
| 1572 |
> |
|
| 1573 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1574 |
> |
// numbers |
| 1575 |
> |
for (int j = 0; j < 3; j++) |
| 1576 |
> |
{ |
| 1577 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1578 |
> |
scaled[j] += 0.5; |
| 1579 |
> |
} |
| 1580 |
> |
|
| 1581 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1582 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1583 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1584 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1585 |
> |
|
| 1586 |
> |
// find single index of this cell: |
| 1587 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1588 |
> |
|
| 1589 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1590 |
> |
cellListRow_[cellIndex].push_back(i); |
| 1591 |
> |
} |
| 1592 |
> |
for (int i = 0; i < nGroupsInCol_; i++) |
| 1593 |
> |
{ |
| 1594 |
> |
rs = cgColData.position[i]; |
| 1595 |
> |
|
| 1596 |
> |
// scaled positions relative to the box vectors |
| 1597 |
> |
scaled = invHmat * rs; |
| 1598 |
> |
|
| 1599 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1600 |
> |
// numbers |
| 1601 |
> |
for (int j = 0; j < 3; j++) |
| 1602 |
> |
{ |
| 1603 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1604 |
> |
scaled[j] += 0.5; |
| 1605 |
> |
} |
| 1606 |
> |
|
| 1607 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1608 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1609 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1610 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1611 |
> |
|
| 1612 |
> |
// find single index of this cell: |
| 1613 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1614 |
> |
|
| 1615 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1616 |
> |
cellListCol_[cellIndex].push_back(i); |
| 1617 |
> |
} |
| 1618 |
> |
#else |
| 1619 |
> |
for (int i = 0; i < nGroups_; i++) |
| 1620 |
> |
{ |
| 1621 |
> |
rs = snap_->cgData.position[i]; |
| 1622 |
> |
|
| 1623 |
> |
// scaled positions relative to the box vectors |
| 1624 |
> |
scaled = invHmat * rs; |
| 1625 |
> |
|
| 1626 |
> |
// wrap the vector back into the unit box by subtracting integer box |
| 1627 |
> |
// numbers |
| 1628 |
> |
for (int j = 0; j < 3; j++) |
| 1629 |
> |
{ |
| 1630 |
> |
scaled[j] -= roundMe(scaled[j]); |
| 1631 |
> |
scaled[j] += 0.5; |
| 1632 |
> |
} |
| 1633 |
> |
|
| 1634 |
> |
// find xyz-indices of cell that cutoffGroup is in. |
| 1635 |
> |
whichCell.x() = nCells_.x() * scaled.x(); |
| 1636 |
> |
whichCell.y() = nCells_.y() * scaled.y(); |
| 1637 |
> |
whichCell.z() = nCells_.z() * scaled.z(); |
| 1638 |
> |
|
| 1639 |
> |
// find single index of this cell: |
| 1640 |
> |
cellIndex = Vlinear(whichCell, nCells_); |
| 1641 |
> |
|
| 1642 |
> |
// add this cutoff group to the list of groups in this cell; |
| 1643 |
> |
cellList_[cellIndex].push_back(i); |
| 1644 |
> |
} |
| 1645 |
> |
#endif |
| 1646 |
> |
|
| 1647 |
> |
for (int m1z = 0; m1z < nCells_.z(); m1z++) |
| 1648 |
> |
{ |
| 1649 |
> |
for (int m1y = 0; m1y < nCells_.y(); m1y++) |
| 1650 |
> |
{ |
| 1651 |
> |
for (int m1x = 0; m1x < nCells_.x(); m1x++) |
| 1652 |
> |
{ |
| 1653 |
> |
Vector3i m1v(m1x, m1y, m1z); |
| 1654 |
> |
int m1 = Vlinear(m1v, nCells_); |
| 1655 |
> |
|
| 1656 |
> |
for (vector<Vector3i>::iterator os = cellOffsets_.begin(); os != cellOffsets_.end(); ++os) |
| 1657 |
> |
{ |
| 1658 |
> |
|
| 1659 |
> |
Vector3i m2v = m1v + (*os); |
| 1660 |
> |
|
| 1661 |
> |
if (m2v.x() >= nCells_.x()) |
| 1662 |
> |
{ |
| 1663 |
> |
m2v.x() = 0; |
| 1664 |
> |
} else if (m2v.x() < 0) |
| 1665 |
> |
{ |
| 1666 |
> |
m2v.x() = nCells_.x() - 1; |
| 1667 |
> |
} |
| 1668 |
> |
|
| 1669 |
> |
if (m2v.y() >= nCells_.y()) |
| 1670 |
> |
{ |
| 1671 |
> |
m2v.y() = 0; |
| 1672 |
> |
} else if (m2v.y() < 0) |
| 1673 |
> |
{ |
| 1674 |
> |
m2v.y() = nCells_.y() - 1; |
| 1675 |
> |
} |
| 1676 |
> |
|
| 1677 |
> |
if (m2v.z() >= nCells_.z()) |
| 1678 |
> |
{ |
| 1679 |
> |
m2v.z() = 0; |
| 1680 |
> |
} else if (m2v.z() < 0) |
| 1681 |
> |
{ |
| 1682 |
> |
m2v.z() = nCells_.z() - 1; |
| 1683 |
> |
} |
| 1684 |
> |
|
| 1685 |
> |
int m2 = Vlinear(m2v, nCells_); |
| 1686 |
> |
|
| 1687 |
> |
#ifdef IS_MPI |
| 1688 |
> |
for (vector<int>::iterator j1 = cellListRow_[m1].begin(); |
| 1689 |
> |
j1 != cellListRow_[m1].end(); ++j1) |
| 1690 |
> |
{ |
| 1691 |
> |
for (vector<int>::iterator j2 = cellListCol_[m2].begin(); |
| 1692 |
> |
j2 != cellListCol_[m2].end(); ++j2) |
| 1693 |
> |
{ |
| 1694 |
> |
|
| 1695 |
> |
// In parallel, we need to visit *all* pairs of row & |
| 1696 |
> |
// column indicies and will truncate later on. |
| 1697 |
> |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 1698 |
> |
snap_->wrapVector(dr); |
| 1699 |
> |
cuts = getGroupCutoffs( (*j1), (*j2) ); |
| 1700 |
> |
if (dr.lengthSquare() < cuts.third) |
| 1701 |
> |
{ |
| 1702 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1703 |
> |
} |
| 1704 |
> |
} |
| 1705 |
> |
} |
| 1706 |
> |
#else |
| 1707 |
> |
|
| 1708 |
> |
for (vector<int>::iterator j1 = cellList_[m1].begin(); j1 != cellList_[m1].end(); ++j1) |
| 1709 |
> |
{ |
| 1710 |
> |
for (vector<int>::iterator j2 = cellList_[m2].begin(); j2 != cellList_[m2].end(); ++j2) |
| 1711 |
> |
{ |
| 1712 |
> |
|
| 1713 |
> |
// Always do this if we're in different cells or if |
| 1714 |
> |
// we're in the same cell and the global index of the |
| 1715 |
> |
// j2 cutoff group is less than the j1 cutoff group |
| 1716 |
> |
|
| 1717 |
> |
if (m2 != m1 || (*j2) < (*j1)) |
| 1718 |
> |
{ |
| 1719 |
> |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 1720 |
> |
snap_->wrapVector(dr); |
| 1721 |
> |
cuts = getGroupCutoffs((*j1), (*j2)); |
| 1722 |
> |
if (dr.lengthSquare() < cuts.third) |
| 1723 |
> |
{ |
| 1724 |
> |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 1725 |
> |
} |
| 1726 |
> |
} |
| 1727 |
> |
} |
| 1728 |
> |
} |
| 1729 |
> |
#endif |
| 1730 |
> |
} |
| 1731 |
> |
} |
| 1732 |
> |
} |
| 1733 |
> |
} |
| 1734 |
> |
} else |
| 1735 |
> |
{ |
| 1736 |
> |
// branch to do all cutoff group pairs |
| 1737 |
> |
#ifdef IS_MPI |
| 1738 |
> |
for (int j1 = 0; j1 < nGroupsInRow_; j1++) |
| 1739 |
> |
{ |
| 1740 |
> |
for (int j2 = 0; j2 < nGroupsInCol_; j2++) |
| 1741 |
> |
{ |
| 1742 |
> |
dr = cgColData.position[j2] - cgRowData.position[j1]; |
| 1743 |
> |
snap_->wrapVector(dr); |
| 1744 |
> |
cuts = getGroupCutoffs( j1, j2 ); |
| 1745 |
> |
if (dr.lengthSquare() < cuts.third) |
| 1746 |
> |
{ |
| 1747 |
> |
neighborList.push_back(make_pair(j1, j2)); |
| 1748 |
> |
} |
| 1749 |
> |
} |
| 1750 |
> |
} |
| 1751 |
> |
#else |
| 1752 |
> |
for (int j1 = 0; j1 < nGroups_ - 1; j1++) |
| 1753 |
> |
{ |
| 1754 |
> |
for (int j2 = j1 + 1; j2 < nGroups_; j2++) |
| 1755 |
> |
{ |
| 1756 |
> |
dr = snap_->cgData.position[j2] - snap_->cgData.position[j1]; |
| 1757 |
> |
snap_->wrapVector(dr); |
| 1758 |
> |
cuts = getGroupCutoffs(j1, j2); |
| 1759 |
> |
if (dr.lengthSquare() < cuts.third) |
| 1760 |
> |
{ |
| 1761 |
> |
neighborList.push_back(make_pair(j1, j2)); |
| 1762 |
> |
} |
| 1763 |
> |
} |
| 1764 |
> |
} |
| 1765 |
> |
#endif |
| 1766 |
> |
} |
| 1767 |
> |
|
| 1768 |
> |
// save the local cutoff group positions for the check that is |
| 1769 |
> |
// done on each loop: |
| 1770 |
> |
saved_CG_positions_.clear(); |
| 1771 |
> |
for (int i = 0; i < nGroups_; i++) |
| 1772 |
> |
saved_CG_positions_.push_back(snap_->cgData.position[i]); |
| 1773 |
> |
|
| 1774 |
> |
return neighborList; |
| 1775 |
> |
} |
| 1776 |
|
} //end namespace OpenMD |
