| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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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 |
|
*/ |
| 42 |
|
|
| 43 |
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#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 56 |
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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) {}; |
| 59 |
> |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
| 60 |
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|
| 61 |
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void distributeInitialData(); |
| 62 |
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void zeroWorkArrays(); |
| 70 |
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|
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// group bookkeeping |
| 72 |
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groupCutoffs getGroupCutoffs(int cg1, int cg2); |
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+ |
Vector3d getGroupVelocityColumn(int cg2); |
| 74 |
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|
| 75 |
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// Group->atom bookkeeping |
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vector<int> getAtomsInGroupRow(int cg1); |
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bool excludeAtomPair(int atom1, int atom2); |
| 93 |
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void addForceToAtomRow(int atom1, Vector3d fg); |
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void addForceToAtomColumn(int atom2, Vector3d fg); |
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+ |
Vector3d getAtomVelocityColumn(int atom2); |
| 96 |
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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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vector<int> groupToGtype; |
| 110 |
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|
| 111 |
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#ifdef IS_MPI |
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< |
DataStorage atomRowData; |
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< |
DataStorage atomColData; |
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> |
DataStorage atomRowData; DataStorage atomColData; |
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DataStorage cgRowData; |
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DataStorage cgColData; |
| 115 |
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|
| 118 |
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int nGroupsInRow_; |
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int nGroupsInCol_; |
| 120 |
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|
| 121 |
< |
Communicator<Row, int>* AtomCommIntRow; |
| 122 |
< |
Communicator<Row, RealType>* AtomCommRealRow; |
| 121 |
< |
Communicator<Row, Vector3d>* AtomCommVectorRow; |
| 122 |
< |
Communicator<Row, Mat3x3d>* AtomCommMatrixRow; |
| 123 |
< |
Communicator<Row, potVec>* AtomCommPotRow; |
| 121 |
> |
Communicator<Row> rowComm; |
| 122 |
> |
Communicator<Column> colComm; |
| 123 |
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|
| 124 |
< |
Communicator<Column, int>* AtomCommIntColumn; |
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< |
Communicator<Column, RealType>* AtomCommRealColumn; |
| 126 |
< |
Communicator<Column, Vector3d>* AtomCommVectorColumn; |
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< |
Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
| 128 |
< |
Communicator<Column, potVec>* AtomCommPotColumn; |
| 124 |
> |
Plan<int>* AtomPlanIntRow; |
| 125 |
> |
Plan<RealType>* AtomPlanRealRow; |
| 126 |
> |
Plan<Vector3d>* AtomPlanVectorRow; |
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> |
Plan<Mat3x3d>* AtomPlanMatrixRow; |
| 128 |
> |
Plan<potVec>* AtomPlanPotRow; |
| 129 |
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|
| 130 |
< |
Communicator<Row, int>* cgCommIntRow; |
| 131 |
< |
Communicator<Row, Vector3d>* cgCommVectorRow; |
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< |
Communicator<Column, int>* cgCommIntColumn; |
| 133 |
< |
Communicator<Column, Vector3d>* cgCommVectorColumn; |
| 130 |
> |
Plan<int>* AtomPlanIntColumn; |
| 131 |
> |
Plan<RealType>* AtomPlanRealColumn; |
| 132 |
> |
Plan<Vector3d>* AtomPlanVectorColumn; |
| 133 |
> |
Plan<Mat3x3d>* AtomPlanMatrixColumn; |
| 134 |
> |
Plan<potVec>* AtomPlanPotColumn; |
| 135 |
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|
| 136 |
+ |
Plan<int>* cgPlanIntRow; |
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+ |
Plan<Vector3d>* cgPlanVectorRow; |
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+ |
Plan<int>* cgPlanIntColumn; |
| 139 |
+ |
Plan<Vector3d>* cgPlanVectorColumn; |
| 140 |
+ |
|
| 141 |
|
// work arrays for assembling potential energy |
| 142 |
|
vector<potVec> pot_row; |
| 143 |
|
vector<potVec> pot_col; |
| 151 |
|
vector<int> AtomRowToGlobal; |
| 152 |
|
vector<int> AtomColToGlobal; |
| 153 |
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|
| 154 |
+ |
public: |
| 155 |
|
vector<int> cgRowToGlobal; |
| 156 |
|
vector<int> cgColToGlobal; |
| 157 |
|
|
| 158 |
+ |
private: |
| 159 |
|
vector<RealType> groupCutoffRow; |
| 160 |
|
vector<RealType> groupCutoffCol; |
| 161 |
|
vector<int> groupColToGtype; |
