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/** |
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* @file ForceDecomposition.cpp |
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* @author Charles Vardeman <cvardema.at.nd.edu> |
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* @date 08/18/2010 |
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* @time 11:56am |
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* @version 1.0 |
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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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* @section LICENSE |
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* Copyright (c) 2010 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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* [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/ForceDecomposition.hpp" |
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#include "parallel/Communicator.hpp" |
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#include "math/SquareMatrix3.hpp" |
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namespace OpenMD { |
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/* -*- c++ -*- */ |
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#include "config.h" |
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#include <stdlib.h> |
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void ForceDecomposition::distributeInitialData() { |
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif |
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#include <iostream> |
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#include <vector> |
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#include <algorithm> |
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#include <cmath> |
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#include "parallel/ForceDecomposition.hpp" |
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int nAtoms; |
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int nGroups; |
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AtomCommRealI = new Communicator<Row,RealType>(nAtoms); |
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AtomCommVectorI = new Communicator<Row,Vector3d>(nAtoms); |
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AtomCommMatrixI = new Communicator<Row,Mat3x3d>(nAtoms); |
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|
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using namespace std; |
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using namespace OpenMD; |
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AtomCommRealJ = new Communicator<Column,RealType>(nAtoms); |
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AtomCommVectorJ = new Communicator<Column,Vector3d>(nAtoms); |
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AtomCommMatrixJ = new Communicator<Column,Mat3x3d>(nAtoms); |
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|
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//__static |
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#ifdef IS_MPI |
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static vector<MPI:Comm> communictors; |
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cgCommVectorI = new Communicator<Row,Vector3d>(nGroups); |
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cgCommVectorJ = new Communicator<Column,Vector3d>(nGroups); |
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// more to come |
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#endif |
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} |
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//____ MPITypeTraits |
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template<typename T> |
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struct MPITypeTraits; |
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void ForceDecomposition::distributeData() { |
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#ifdef IS_MPI |
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template<> |
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struct MPITypeTraits<RealType> { |
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static const MPI::Datatype datatype; |
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}; |
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const MPI_Datatype MPITypeTraits<RealType>::datatype = MY_MPI_REAL; |
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template<> |
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struct MPITypeTraits<int> { |
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static const MPI::Datatype datatype; |
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}; |
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const MPI::Datatype MPITypeTraits<int>::datatype = MPI_INT; |
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#endif |
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|
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/** |
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* Constructor for ForceDecomposition Parallel Decomposition Method |
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* Will try to construct a symmetric grid of processors. Ideally, the |
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* number of processors will be a square ex: 4, 9, 16, 25. |
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* |
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*/ |
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ForceDecomposition::ForceDecomposition() { |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
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// gather up the atomic positions |
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AtomCommVectorI->gather(snap->atomData.position, |
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snap->atomIData.position); |
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AtomCommVectorJ->gather(snap->atomData.position, |
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snap->atomJData.position); |
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// gather up the cutoff group positions |
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cgCommVectorI->gather(snap->cgData.position, |
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snap->cgIData.position); |
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cgCommVectorJ->gather(snap->cgData.position, |
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snap->cgJData.position); |
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|
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// if needed, gather the atomic rotation matrices |
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if (snap->atomData.getStorageLayout() & DataStorage::dslAmat) { |
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AtomCommMatrixI->gather(snap->atomData.aMat, |
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snap->atomIData.aMat); |
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AtomCommMatrixJ->gather(snap->atomData.aMat, |
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snap->atomJData.aMat); |
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} |
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// if needed, gather the atomic eletrostatic frames |
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if (snap->atomData.getStorageLayout() & DataStorage::dslElectroFrame) { |
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AtomCommMatrixI->gather(snap->atomData.electroFrame, |
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snap->atomIData.electroFrame); |
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AtomCommMatrixJ->gather(snap->atomData.electroFrame, |
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snap->atomJData.electroFrame); |
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} |
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#endif |
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} |
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|
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void ForceDecomposition::collectIntermediateData() { |
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#ifdef IS_MPI |
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int nProcs = MPI::COMM_WORLD.Get_size(); |
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int worldRank = MPI::COMM_WORLD.Get_rank(); |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
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if (snap->atomData.getStorageLayout() & DataStorage::dslDensity) { |
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AtomCommRealI->scatter(snap->atomIData.density, |
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snap->atomData.density); |
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std::vector<RealType> rho_tmp; |
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int n = snap->getNumberOfAtoms(); |
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rho_tmp.reserve( n ); |
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AtomCommRealJ->scatter(snap->atomJData.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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// First time through, construct column stride. |
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if (communicators.size() == 0) |
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{ |
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int nColumnsMax = (int) round(sqrt((float) nProcs)); |
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for (int i = 0; i < nProcs; ++i) |
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{ |
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if (nProcs%i==0) nColumns=i; |
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} |
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|
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void ForceDecomposition::distributeIntermediateData() { |
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#ifdef IS_MPI |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
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if (snap->atomData.getStorageLayout() & DataStorage::dslFunctional) { |
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AtomCommRealI->gather(snap->atomData.functional, |
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snap->atomIData.functional); |
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AtomCommRealJ->gather(snap->atomData.functional, |
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snap->atomJData.functional); |
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} |
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int nRows = nProcs/nColumns; |
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myRank_ = (int) worldRank%nColumns; |
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if (snap->atomData.getStorageLayout() & DataStorage::dslFunctionalDerivative) { |
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AtomCommRealI->gather(snap->atomData.functionalDerivative, |
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snap->atomIData.functionalDerivative); |
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AtomCommRealJ->gather(snap->atomData.functionalDerivative, |
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snap->atomJData.functionalDerivative); |
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} |
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#endif |
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} |
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else |
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{ |
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myRank_ = myRank/nColumns; |
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} |
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MPI::Comm newComm = MPI:COMM_WORLD.Split(myRank_,0); |
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isColumn_ = false; |
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} |
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void ForceDecomposition::collectData() { |
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#ifdef IS_MPI |
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Snapshot* snap = sman_->getCurrentSnapshot(); |
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int n = snap->getNumberOfAtoms(); |
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ForceDecomposition::gather(sendbuf, receivebuf){ |
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communicators(myIndex_).Allgatherv(); |
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} |
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std::vector<Vector3d> frc_tmp; |
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frc_tmp.reserve( n ); |
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AtomCommVectorI->scatter(snap->atomIData.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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AtomCommVectorJ->scatter(snap->atomJData.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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if (snap->atomData.getStorageLayout() & DataStorage::dslTorque) { |
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std::vector<Vector3d> trq_tmp; |
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trq_tmp.reserve( n ); |
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AtomCommVectorI->scatter(snap->atomIData.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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AtomCommVectorJ->scatter(snap->atomJData.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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// Still need pot! |
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ForceDecomposition::scatter(sbuffer, rbuffer){ |
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communicators(myIndex_).Reduce_scatter(sbuffer, recevbuf. recvcounts, MPI::DOUBLE, MPI::SUM); |
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} |
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#endif |
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} |
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|
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} //end namespace OpenMD |
