| 36 |
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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). |
| 39 |
< |
* [4] Vardeman & Gezelter, in progress (2009). |
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> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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class ForceMatrixDecomposition : public ForceDecomposition { |
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public: |
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< |
ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(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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// neighbor list routines |
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bool checkNeighborList(); |
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vector<pair<int, int> > buildNeighborList(); |
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|
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// group bookkeeping |
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< |
pair<int, int> getGroupTypes(int cg1, int cg2); |
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> |
groupCutoffs getGroupCutoffs(int cg1, int cg2); |
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|
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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 getMfactRow(int atom1); |
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< |
RealType getMfactColumn(int atom2); |
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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 getInteratomicVector(int atom1, int atom2); |
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|
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// atom bookkeeping |
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< |
vector<int> getAtomList(); |
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< |
vector<int> getSkipsForAtom(int atom1); |
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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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< |
InteractionData fillInteractionData(int atom1, int atom2); |
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< |
InteractionData fillSkipData(int atom1, int atom2); |
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< |
SelfData fillSelfData(int atom1); |
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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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private: |
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< |
SnapshotManager* sman_; |
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< |
Snapshot* snap_; |
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< |
int storageLayout_; |
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< |
vector<Vector3i> Cells; |
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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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DataStorage atomRowData; |
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int nGroupsInRow_; |
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int nGroupsInCol_; |
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|
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< |
Communicator<Row, int>* AtomCommIntRow; |
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< |
Communicator<Row, RealType>* AtomCommRealRow; |
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< |
Communicator<Row, Vector3d>* AtomCommVectorRow; |
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< |
Communicator<Row, Mat3x3d>* AtomCommMatrixRow; |
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> |
Communicator<Row> rowComm; |
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> |
Communicator<Column> colComm; |
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|
| 123 |
< |
Communicator<Column, int>* AtomCommIntColumn; |
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< |
Communicator<Column, RealType>* AtomCommRealColumn; |
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< |
Communicator<Column, Vector3d>* AtomCommVectorColumn; |
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< |
Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
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> |
Plan<int>* AtomPlanIntRow; |
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> |
Plan<RealType>* AtomPlanRealRow; |
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> |
Plan<Vector3d>* AtomPlanVectorRow; |
| 126 |
> |
Plan<Mat3x3d>* AtomPlanMatrixRow; |
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> |
Plan<potVec>* AtomPlanPotRow; |
| 128 |
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|
| 129 |
< |
Communicator<Row, int>* cgCommIntRow; |
| 130 |
< |
Communicator<Row, Vector3d>* cgCommVectorRow; |
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< |
Communicator<Column, int>* cgCommIntColumn; |
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< |
Communicator<Column, Vector3d>* cgCommVectorColumn; |
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> |
Plan<int>* AtomPlanIntColumn; |
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> |
Plan<RealType>* AtomPlanRealColumn; |
| 131 |
> |
Plan<Vector3d>* AtomPlanVectorColumn; |
| 132 |
> |
Plan<Mat3x3d>* AtomPlanMatrixColumn; |
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> |
Plan<potVec>* AtomPlanPotColumn; |
| 134 |
|
|
| 135 |
< |
vector<vector<RealType> > pot_row; |
| 136 |
< |
vector<vector<RealType> > pot_col; |
| 135 |
> |
Plan<int>* cgPlanIntRow; |
| 136 |
> |
Plan<Vector3d>* cgPlanVectorRow; |
| 137 |
> |
Plan<int>* cgPlanIntColumn; |
| 138 |
> |
Plan<Vector3d>* cgPlanVectorColumn; |
| 139 |
> |
|
| 140 |
> |
// work arrays for assembling potential energy |
| 141 |
> |
vector<potVec> pot_row; |
| 142 |
> |
vector<potVec> pot_col; |
| 143 |
> |
|
| 144 |
|
vector<int> identsRow; |
| 145 |
|
vector<int> identsCol; |
| 146 |
|
|
| 147 |
< |
vector<int> AtomLocalToGlobal; |
| 147 |
> |
vector<AtomType*> atypesRow; |
| 148 |
> |
vector<AtomType*> atypesCol; |
| 149 |
> |
|
| 150 |
|
vector<int> AtomRowToGlobal; |
| 151 |
|
vector<int> AtomColToGlobal; |
| 152 |
< |
vector<int> cgLocalToGlobal; |
| 152 |
> |
|
| 153 |
> |
public: |
| 154 |
|
vector<int> cgRowToGlobal; |
| 155 |
|
vector<int> cgColToGlobal; |
| 156 |
|
|
| 157 |
< |
vector<vector<int> > CellListRow; |
| 158 |
< |
vector<vector<int> > CellListCol; |
| 159 |
< |
#else |
| 160 |
< |
vector<vector<int> > CellList; |
| 157 |
> |
private: |
| 158 |
> |
vector<RealType> groupCutoffRow; |
| 159 |
> |
vector<RealType> groupCutoffCol; |
| 160 |
> |
vector<int> groupColToGtype; |
| 161 |
> |
vector<int> groupRowToGtype; |
| 162 |
> |
|
| 163 |
> |
vector<vector<int> > cellListRow_; |
| 164 |
> |
vector<vector<int> > cellListCol_; |
| 165 |
> |
|
| 166 |
> |
vector<vector<int> > groupListRow_; |
| 167 |
> |
vector<vector<int> > groupListCol_; |
| 168 |
> |
|
| 169 |
> |
vector<RealType> massFactorsRow; |
| 170 |
> |
vector<RealType> massFactorsCol; |
| 171 |
|
#endif |
| 148 |
– |
vector<RealType> pot_local; |
| 172 |
|
|
| 173 |
|
}; |
| 174 |
|
|
