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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#include "parallel/ForceMatrixDecomposition.hpp" |
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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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nLocal_ = snap_->getNumberOfAtoms(); |
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nGroups_ = snap_->getNumberOfCutoffGroups(); |
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|
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#ifdef IS_MPI |
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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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nAtomsInRow_ = AtomCommIntRow->getSize(); |
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nAtomsInCol_ = AtomCommIntColumn->getSize(); |
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nGroupsInRow_ = cgCommIntRow->getSize(); |
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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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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]; |
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#else |
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d = snap_->cgData.position[cg1] - snap_->atomData.position[atom1]; |
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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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|
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#ifdef IS_MPI |
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d = cgColData.position[cg2] - atomColData.position[atom2]; |
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#else |
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d = snap_->cgData.position[cg2] - snap_->atomData.position[atom2]; |
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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::getInteratomicVector(int atom1, int atom2){ |
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Vector3d d; |
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|
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#ifdef IS_MPI |
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d = atomColData.position[atom2] - atomRowData.position[atom1]; |
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#else |
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d = snap_->atomData.position[atom2] - snap_->atomData.position[atom1]; |
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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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void ForceMatrixDecomposition::addForceToAtomRow(int atom1, Vector3d fg){ |
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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; |
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#endif |
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} |
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|
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void ForceMatrixDecomposition::addForceToAtomColumn(int atom2, Vector3d fg){ |
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#ifdef IS_MPI |
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atomColData.force[atom2] += fg; |
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#else |
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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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// filling interaction blocks with pointers |
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InteractionData ForceMatrixDecomposition::fillInteractionData(int atom1, int atom2) { |
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InteractionData idat; |
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|
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#ifdef IS_MPI |
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if (storageLayout_ & DataStorage::dslAmat) { |
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idat.A1 = &(atomRowData.aMat[atom1]); |
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idat.A2 = &(atomColData.aMat[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslElectroFrame) { |
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idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
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idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslTorque) { |
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idat.t1 = &(atomRowData.torque[atom1]); |
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idat.t2 = &(atomColData.torque[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslDensity) { |
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idat.rho1 = &(atomRowData.density[atom1]); |
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idat.rho2 = &(atomColData.density[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
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idat.dfrho1 = &(atomRowData.functionalDerivative[atom1]); |
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idat.dfrho2 = &(atomColData.functionalDerivative[atom2]); |
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} |
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#else |
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if (storageLayout_ & DataStorage::dslAmat) { |
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idat.A1 = &(snap_->atomData.aMat[atom1]); |
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idat.A2 = &(snap_->atomData.aMat[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslElectroFrame) { |
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idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
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idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslTorque) { |
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idat.t1 = &(snap_->atomData.torque[atom1]); |
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idat.t2 = &(snap_->atomData.torque[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslDensity) { |
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idat.rho1 = &(snap_->atomData.density[atom1]); |
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idat.rho2 = &(snap_->atomData.density[atom2]); |
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} |
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|
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if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
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idat.dfrho1 = &(snap_->atomData.functionalDerivative[atom1]); |
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idat.dfrho2 = &(snap_->atomData.functionalDerivative[atom2]); |
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} |
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#endif |
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return idat; |
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} |
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|
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InteractionData ForceMatrixDecomposition::fillSkipData(int atom1, int atom2){ |
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|
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InteractionData idat; |
| 379 |
#ifdef IS_MPI |
| 380 |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
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idat.eFrame1 = &(atomRowData.electroFrame[atom1]); |
| 382 |
idat.eFrame2 = &(atomColData.electroFrame[atom2]); |
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} |
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if (storageLayout_ & DataStorage::dslTorque) { |
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idat.t1 = &(atomRowData.torque[atom1]); |
| 386 |
idat.t2 = &(atomColData.torque[atom2]); |
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} |
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if (storageLayout_ & DataStorage::dslForce) { |
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idat.t1 = &(atomRowData.force[atom1]); |
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idat.t2 = &(atomColData.force[atom2]); |
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} |
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#else |
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if (storageLayout_ & DataStorage::dslElectroFrame) { |
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idat.eFrame1 = &(snap_->atomData.electroFrame[atom1]); |
| 395 |
idat.eFrame2 = &(snap_->atomData.electroFrame[atom2]); |
| 396 |
} |
| 397 |
if (storageLayout_ & DataStorage::dslTorque) { |
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idat.t1 = &(snap_->atomData.torque[atom1]); |
| 399 |
idat.t2 = &(snap_->atomData.torque[atom2]); |
| 400 |
} |
| 401 |
if (storageLayout_ & DataStorage::dslForce) { |
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idat.t1 = &(snap_->atomData.force[atom1]); |
| 403 |
idat.t2 = &(snap_->atomData.force[atom2]); |
| 404 |
} |
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#endif |
| 406 |
|
| 407 |
} |
| 408 |
|
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SelfData ForceMatrixDecomposition::fillSelfData(int atom1) { |
| 410 |
SelfData sdat; |
| 411 |
// Still Missing atype, skippedCharge, potVec pot, |
| 412 |
if (storageLayout_ & DataStorage::dslElectroFrame) { |
| 413 |
sdat.eFrame = &(snap_->atomData.electroFrame[atom1]); |
| 414 |
} |
| 415 |
|
| 416 |
if (storageLayout_ & DataStorage::dslTorque) { |
| 417 |
sdat.t = &(snap_->atomData.torque[atom1]); |
| 418 |
} |
| 419 |
|
| 420 |
if (storageLayout_ & DataStorage::dslDensity) { |
| 421 |
sdat.rho = &(snap_->atomData.density[atom1]); |
| 422 |
} |
| 423 |
|
| 424 |
if (storageLayout_ & DataStorage::dslFunctional) { |
| 425 |
sdat.frho = &(snap_->atomData.functional[atom1]); |
| 426 |
} |
| 427 |
|
| 428 |
if (storageLayout_ & DataStorage::dslFunctionalDerivative) { |
| 429 |
sdat.dfrhodrho = &(snap_->atomData.functionalDerivative[atom1]); |
| 430 |
} |
| 431 |
|
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return sdat; |
| 433 |
} |
| 434 |
|
| 435 |
|
| 436 |
|
| 437 |
/* |
| 438 |
* buildNeighborList |
| 439 |
* |
| 440 |
* first element of pair is row-indexed CutoffGroup |
| 441 |
* second element of pair is column-indexed CutoffGroup |
| 442 |
*/ |
| 443 |
vector<pair<int, int> > ForceMatrixDecomposition::buildNeighborList() { |
| 444 |
|
| 445 |
vector<pair<int, int> > neighborList; |
| 446 |
#ifdef IS_MPI |
| 447 |
CellListRow.clear(); |
| 448 |
CellListCol.clear(); |
| 449 |
#else |
| 450 |
CellList.clear(); |
| 451 |
#endif |
| 452 |
|
| 453 |
// dangerous to not do error checking. |
| 454 |
RealType skinThickness_ = info_->getSimParams()->getSkinThickness(); |
| 455 |
RealType rCut_; |
| 456 |
|
| 457 |
RealType rList_ = (rCut_ + skinThickness_); |
| 458 |
RealType rl2 = rList_ * rList_; |
| 459 |
Snapshot* snap_ = sman_->getCurrentSnapshot(); |
| 460 |
Mat3x3d Hmat = snap_->getHmat(); |
| 461 |
Vector3d Hx = Hmat.getColumn(0); |
| 462 |
Vector3d Hy = Hmat.getColumn(1); |
| 463 |
Vector3d Hz = Hmat.getColumn(2); |
| 464 |
Vector3i nCells; |
| 465 |
|
| 466 |
nCells.x() = (int) ( Hx.length() )/ rList_; |
| 467 |
nCells.y() = (int) ( Hy.length() )/ rList_; |
| 468 |
nCells.z() = (int) ( Hz.length() )/ rList_; |
| 469 |
|
| 470 |
Mat3x3d invHmat = snap_->getInvHmat(); |
| 471 |
Vector3d rs, scaled, dr; |
| 472 |
Vector3i whichCell; |
| 473 |
int cellIndex; |
| 474 |
|
| 475 |
#ifdef IS_MPI |
| 476 |
for (int i = 0; i < nGroupsInRow_; i++) { |
| 477 |
rs = cgRowData.position[i]; |
| 478 |
// scaled positions relative to the box vectors |
| 479 |
scaled = invHmat * rs; |
| 480 |
// wrap the vector back into the unit box by subtracting integer box |
| 481 |
// numbers |
| 482 |
for (int j = 0; j < 3; j++) |
| 483 |
scaled[j] -= roundMe(scaled[j]); |
| 484 |
|
| 485 |
// find xyz-indices of cell that cutoffGroup is in. |
| 486 |
whichCell.x() = nCells.x() * scaled.x(); |
| 487 |
whichCell.y() = nCells.y() * scaled.y(); |
| 488 |
whichCell.z() = nCells.z() * scaled.z(); |
| 489 |
|
| 490 |
// find single index of this cell: |
| 491 |
cellIndex = Vlinear(whichCell, nCells); |
| 492 |
// add this cutoff group to the list of groups in this cell; |
| 493 |
CellListRow[cellIndex].push_back(i); |
| 494 |
} |
| 495 |
|
| 496 |
for (int i = 0; i < nGroupsInCol_; i++) { |
| 497 |
rs = cgColData.position[i]; |
| 498 |
// scaled positions relative to the box vectors |
| 499 |
scaled = invHmat * rs; |
| 500 |
// wrap the vector back into the unit box by subtracting integer box |
| 501 |
// numbers |
| 502 |
for (int j = 0; j < 3; j++) |
| 503 |
scaled[j] -= roundMe(scaled[j]); |
| 504 |
|
| 505 |
// find xyz-indices of cell that cutoffGroup is in. |
| 506 |
whichCell.x() = nCells.x() * scaled.x(); |
| 507 |
whichCell.y() = nCells.y() * scaled.y(); |
| 508 |
whichCell.z() = nCells.z() * scaled.z(); |
| 509 |
|
| 510 |
// find single index of this cell: |
| 511 |
cellIndex = Vlinear(whichCell, nCells); |
| 512 |
// add this cutoff group to the list of groups in this cell; |
| 513 |
CellListCol[cellIndex].push_back(i); |
| 514 |
} |
| 515 |
#else |
| 516 |
for (int i = 0; i < nGroups_; i++) { |
| 517 |
rs = snap_->cgData.position[i]; |
| 518 |
// scaled positions relative to the box vectors |
| 519 |
scaled = invHmat * rs; |
| 520 |
// wrap the vector back into the unit box by subtracting integer box |
| 521 |
// numbers |
| 522 |
for (int j = 0; j < 3; j++) |
| 523 |
scaled[j] -= roundMe(scaled[j]); |
| 524 |
|
| 525 |
// find xyz-indices of cell that cutoffGroup is in. |
| 526 |
whichCell.x() = nCells.x() * scaled.x(); |
| 527 |
whichCell.y() = nCells.y() * scaled.y(); |
| 528 |
whichCell.z() = nCells.z() * scaled.z(); |
| 529 |
|
| 530 |
// find single index of this cell: |
| 531 |
cellIndex = Vlinear(whichCell, nCells); |
| 532 |
// add this cutoff group to the list of groups in this cell; |
| 533 |
CellList[cellIndex].push_back(i); |
| 534 |
} |
| 535 |
#endif |
| 536 |
|
| 537 |
|
| 538 |
|
| 539 |
for (int m1z = 0; m1z < nCells.z(); m1z++) { |
| 540 |
for (int m1y = 0; m1y < nCells.y(); m1y++) { |
| 541 |
for (int m1x = 0; m1x < nCells.x(); m1x++) { |
| 542 |
Vector3i m1v(m1x, m1y, m1z); |
| 543 |
int m1 = Vlinear(m1v, nCells); |
| 544 |
for (int offset = 0; offset < nOffset_; offset++) { |
| 545 |
Vector3i m2v = m1v + cellOffsets_[offset]; |
| 546 |
|
| 547 |
if (m2v.x() >= nCells.x()) { |
| 548 |
m2v.x() = 0; |
| 549 |
} else if (m2v.x() < 0) { |
| 550 |
m2v.x() = nCells.x() - 1; |
| 551 |
} |
| 552 |
|
| 553 |
if (m2v.y() >= nCells.y()) { |
| 554 |
m2v.y() = 0; |
| 555 |
} else if (m2v.y() < 0) { |
| 556 |
m2v.y() = nCells.y() - 1; |
| 557 |
} |
| 558 |
|
| 559 |
if (m2v.z() >= nCells.z()) { |
| 560 |
m2v.z() = 0; |
| 561 |
} else if (m2v.z() < 0) { |
| 562 |
m2v.z() = nCells.z() - 1; |
| 563 |
} |
| 564 |
|
| 565 |
int m2 = Vlinear (m2v, nCells); |
| 566 |
|
| 567 |
#ifdef IS_MPI |
| 568 |
for (vector<int>::iterator j1 = CellListRow[m1].begin(); |
| 569 |
j1 != CellListRow[m1].end(); ++j1) { |
| 570 |
for (vector<int>::iterator j2 = CellListCol[m2].begin(); |
| 571 |
j2 != CellListCol[m2].end(); ++j2) { |
| 572 |
|
| 573 |
// Always do this if we're in different cells or if |
| 574 |
// we're in the same cell and the global index of the |
| 575 |
// j2 cutoff group is less than the j1 cutoff group |
| 576 |
|
| 577 |
if (m2 != m1 || cgColToGlobal[(*j2)] < cgRowToGlobal[(*j1)]) { |
| 578 |
dr = cgColData.position[(*j2)] - cgRowData.position[(*j1)]; |
| 579 |
snap_->wrapVector(dr); |
| 580 |
if (dr.lengthSquare() < rl2) { |
| 581 |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 582 |
} |
| 583 |
} |
| 584 |
} |
| 585 |
} |
| 586 |
#else |
| 587 |
for (vector<int>::iterator j1 = CellList[m1].begin(); |
| 588 |
j1 != CellList[m1].end(); ++j1) { |
| 589 |
for (vector<int>::iterator j2 = CellList[m2].begin(); |
| 590 |
j2 != CellList[m2].end(); ++j2) { |
| 591 |
|
| 592 |
// Always do this if we're in different cells or if |
| 593 |
// we're in the same cell and the global index of the |
| 594 |
// j2 cutoff group is less than the j1 cutoff group |
| 595 |
|
| 596 |
if (m2 != m1 || (*j2) < (*j1)) { |
| 597 |
dr = snap_->cgData.position[(*j2)] - snap_->cgData.position[(*j1)]; |
| 598 |
snap_->wrapVector(dr); |
| 599 |
if (dr.lengthSquare() < rl2) { |
| 600 |
neighborList.push_back(make_pair((*j1), (*j2))); |
| 601 |
} |
| 602 |
} |
| 603 |
} |
| 604 |
} |
| 605 |
#endif |
| 606 |
} |
| 607 |
} |
| 608 |
} |
| 609 |
} |
| 610 |
return neighborList; |
| 611 |
} |
| 612 |
} //end namespace OpenMD |
