| 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). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
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*/ |
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|
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#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
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|
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class ForceMatrixDecomposition : public ForceDecomposition { |
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public: |
| 59 |
< |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {}; |
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> |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
| 60 |
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|
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void distributeInitialData(); |
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void zeroWorkArrays(); |
| 86 |
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// atom bookkeeping |
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int getNAtomsInRow(); |
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int getTopologicalDistance(int atom1, int atom2); |
| 89 |
< |
vector<int> getSkipsForAtom(int atom1); |
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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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– |
void fillSkipData(InteractionData &idat, int atom1, int atom2); |
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– |
void unpackSkipData(InteractionData &idat, int atom1, int atom2); |
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|
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private: |
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void createGtypeCutoffMap(); |
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int nGroupsInRow_; |
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int nGroupsInCol_; |
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|
| 120 |
< |
Communicator<Row, int>* AtomCommIntRow; |
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< |
Communicator<Row, RealType>* AtomCommRealRow; |
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< |
Communicator<Row, Vector3d>* AtomCommVectorRow; |
| 123 |
< |
Communicator<Row, Mat3x3d>* AtomCommMatrixRow; |
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< |
Communicator<Row, potVec>* AtomCommPotRow; |
| 120 |
> |
Communicator<Row> rowComm; |
| 121 |
> |
Communicator<Column> colComm; |
| 122 |
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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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< |
Communicator<Column, potVec>* AtomCommPotColumn; |
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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; |
| 128 |
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|
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< |
Communicator<Row, int>* cgCommIntRow; |
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< |
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; |
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> |
Plan<Mat3x3d>* AtomPlanMatrixColumn; |
| 133 |
> |
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; |
| 142 |
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vector<potVec> pot_col; |
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vector<int> AtomRowToGlobal; |
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vector<int> AtomColToGlobal; |
| 152 |
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|
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+ |
public: |
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|
vector<int> cgRowToGlobal; |
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vector<int> cgColToGlobal; |
| 156 |
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|
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+ |
private: |
| 158 |
|
vector<RealType> groupCutoffRow; |
| 159 |
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vector<RealType> groupCutoffCol; |
| 160 |
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vector<int> groupColToGtype; |
