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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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< |
#ifndef PARALLEL_FORCEDECOMPOSITION_HPP |
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< |
#define PARALLEL_FORCEDECOMPOSITION_HPP |
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> |
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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> |
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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|
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< |
#include "Parallel/Decomposition.hpp" |
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> |
#include "parallel/ForceDecomposition.hpp" |
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#include "math/SquareMatrix3.hpp" |
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+ |
#include "brains/Snapshot.hpp" |
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#ifdef IS_MPI |
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< |
#include "Parallel/Communicator.hpp" |
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> |
#include "parallel/Communicator.hpp" |
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#endif |
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using namespace std; |
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namespace OpenMD { |
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|
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< |
class ForceDecomposition : public Decomposition { |
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> |
class ForceMatrixDecomposition : public ForceDecomposition { |
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public: |
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< |
ForceDecomposition(SimInfo* info) : Decomposition(info) {sman_ = info_->getSnapshotManager();} |
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> |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
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> |
|
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void distributeInitialData(); |
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void zeroWorkArrays(); |
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void distributeData(); |
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void collectIntermediateData(); |
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void distributeIntermediateData(); |
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void collectData(); |
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|
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< |
unsigned int getNcutoffGroupsI(); |
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< |
unsigned int getNcutoffGroupsJ(); |
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> |
// neighbor list routines |
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> |
vector<pair<int, int> > buildNeighborList(); |
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> |
// neighbor list routines based on Rapaport |
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> |
vector<vector<CutoffGroup *> > buildLayerBasedNeighborList(); |
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|
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< |
vector<int> getAtomsInGroupI(int whichCGI); |
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< |
vector<int> getAtomsInGroupJ(int whichCGJ); |
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> |
// group bookkeeping |
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> |
groupCutoffs getGroupCutoffs(int cg1, int cg2); |
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|
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< |
AtomType* getAtomTypeI(int whichAtomI); |
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< |
AtomType* getAtomTypeJ(int whichAtomJ); |
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> |
// Group->atom bookkeeping |
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> |
vector<int> getAtomsInGroupRow(int cg1); |
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> |
vector<int> getAtomsInGroupColumn(int cg2); |
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> |
Vector3d getAtomToGroupVectorRow(int atom1, int cg1); |
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> |
Vector3d getAtomToGroupVectorColumn(int atom2, int cg2); |
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> |
RealType getMassFactorRow(int atom1); |
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> |
RealType getMassFactorColumn(int atom2); |
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|
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+ |
// spatial data |
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+ |
Vector3d getIntergroupVector(int cg1, int cg2); |
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+ |
Vector3d getIntergroupVector(CutoffGroup *cg1, CutoffGroup *cg2); |
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+ |
Vector3d getInteratomicVector(int atom1, int atom2); |
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|
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+ |
// atom bookkeeping |
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int getNAtomsInRow(); |
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+ |
int getTopologicalDistance(int atom1, int atom2); |
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+ |
vector<int> getExcludesForAtom(int atom1); |
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+ |
bool skipAtomPair(int atom1, int atom2); |
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+ |
bool excludeAtomPair(int atom1, int atom2); |
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+ |
void addForceToAtomRow(int atom1, Vector3d fg); |
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void addForceToAtomColumn(int atom2, Vector3d fg); |
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|
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+ |
// filling interaction blocks with pointers |
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void fillInteractionData(InteractionData &idat, int atom1, int atom2); |
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+ |
void unpackInteractionData(InteractionData &idat, int atom1, int atom2); |
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|
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+ |
// memory reordering |
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+ |
void reorderGroupCutoffs(vector<int> &order); |
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void reorderPosition(vector<int> &order); |
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void reorderGroupList(vector<int> &order); |
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void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l); |
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|
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private: |
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< |
SnapshotManager* sman_; |
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> |
void createGtypeCutoffMap(); |
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> |
|
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> |
int nLocal_; |
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> |
int nGroups_; |
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> |
vector<int> AtomLocalToGlobal; |
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> |
vector<int> cgLocalToGlobal; |
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> |
vector<RealType> groupCutoff; |
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> |
vector<int> groupToGtype; |
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> |
|
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#ifdef IS_MPI |
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< |
Communicator<Row, int>* AtomCommIntI; |
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< |
Communicator<Row, RealType>* AtomCommRealI; |
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< |
Communicator<Row, Vector3d>* AtomCommVectorI; |
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< |
Communicator<Row, Mat3x3d>* AtomCommMatrixI; |
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> |
DataStorage atomRowData; |
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> |
DataStorage atomColData; |
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> |
DataStorage cgRowData; |
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> |
DataStorage cgColData; |
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|
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< |
Communicator<Column, int>* AtomCommIntJ; |
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< |
Communicator<Column, RealType>* AtomCommRealJ; |
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< |
Communicator<Column, Vector3d>* AtomCommVectorJ; |
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< |
Communicator<Column, Mat3x3d>* AtomCommMatrixJ; |
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> |
int nAtomsInRow_; |
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> |
int nAtomsInCol_; |
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> |
int nGroupsInRow_; |
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> |
int nGroupsInCol_; |
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|
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< |
Communicator<Row, int>* cgCommIntI; |
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< |
Communicator<Row, Vector3d>* cgCommVectorI; |
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< |
Communicator<Column, int>* cgCommIntJ; |
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< |
Communicator<Column, Vector3d>* cgCommVectorJ; |
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> |
Communicator<Row> rowComm; |
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> |
Communicator<Column> colComm; |
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|
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< |
vector<vector<RealType> > pot_row; |
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< |
vector<vector<RealType> > pot_col; |
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< |
vector<int> identRow; |
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< |
vector<int> identCol; |
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> |
Plan<int>* AtomPlanIntRow; |
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> |
Plan<RealType>* AtomPlanRealRow; |
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> |
Plan<Vector3d>* AtomPlanVectorRow; |
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> |
Plan<Mat3x3d>* AtomPlanMatrixRow; |
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> |
Plan<potVec>* AtomPlanPotRow; |
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|
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< |
vector<int> AtomLocalToGlobal; |
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> |
Plan<int>* AtomPlanIntColumn; |
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> |
Plan<RealType>* AtomPlanRealColumn; |
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> |
Plan<Vector3d>* AtomPlanVectorColumn; |
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> |
Plan<Mat3x3d>* AtomPlanMatrixColumn; |
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> |
Plan<potVec>* AtomPlanPotColumn; |
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> |
|
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> |
Plan<int>* cgPlanIntRow; |
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> |
Plan<Vector3d>* cgPlanVectorRow; |
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> |
Plan<int>* cgPlanIntColumn; |
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> |
Plan<Vector3d>* cgPlanVectorColumn; |
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> |
|
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> |
// work arrays for assembling potential energy |
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> |
vector<potVec> pot_row; |
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> |
vector<potVec> pot_col; |
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> |
|
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> |
vector<int> identsRow; |
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> |
vector<int> identsCol; |
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> |
|
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> |
vector<AtomType*> atypesRow; |
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> |
vector<AtomType*> atypesCol; |
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> |
|
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vector<int> AtomRowToGlobal; |
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|
vector<int> AtomColToGlobal; |
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< |
vector<int> cgLocalToGlobal; |
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> |
|
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vector<int> cgRowToGlobal; |
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|
vector<int> cgColToGlobal; |
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+ |
|
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+ |
vector<RealType> groupCutoffRow; |
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+ |
vector<RealType> groupCutoffCol; |
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+ |
vector<int> groupColToGtype; |
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+ |
vector<int> groupRowToGtype; |
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+ |
|
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+ |
vector<vector<int> > cellListRow_; |
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+ |
vector<vector<int> > cellListCol_; |
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+ |
|
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+ |
vector<vector<int> > groupListRow_; |
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+ |
vector<vector<int> > groupListCol_; |
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+ |
|
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+ |
vector<RealType> massFactorsRow; |
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+ |
vector<RealType> massFactorsCol; |
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|
#endif |
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< |
vector<RealType> pot_local; |
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> |
|
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}; |
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|
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} |
