| 91 |
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class ForceDecomposition { |
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public: |
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| 94 |
< |
ForceDecomposition(SimInfo* info); |
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> |
ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
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virtual ~ForceDecomposition() {} |
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virtual void distributeInitialData() = 0; |
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// atom bookkeeping |
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virtual int getNAtomsInRow() = 0; |
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< |
virtual vector<int> getSkipsForRowAtom(int atom1) = 0; |
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> |
virtual vector<int> getSkipsForAtom(int atom1) = 0; |
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virtual bool skipAtomPair(int atom1, int atom2) = 0; |
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virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
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virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
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+ |
virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
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// filling interaction blocks with pointers |
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< |
virtual InteractionData fillInteractionData(int atom1, int atom2) = 0; |
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> |
virtual void fillInteractionData(InteractionData idat, int atom1, int atom2) = 0; |
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virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0; |
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< |
virtual InteractionData fillSkipData(int atom1, int atom2) = 0; |
| 141 |
< |
virtual SelfData fillSelfData(int atom1); |
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> |
virtual void fillSkipData(InteractionData idat, int atom1, int atom2) = 0; |
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> |
virtual void fillSelfData(SelfData sdat, int atom1); |
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protected: |
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SimInfo* info_; |
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RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
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RealType largestRcut_; |
| 153 |
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| 154 |
< |
map<pair<int, int>, int> topoDist; //< topoDist gives the |
| 155 |
< |
//topological distance between |
| 156 |
< |
//two atomic sites. This |
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< |
//declaration is agnostic |
| 158 |
< |
//regarding the parallel |
| 159 |
< |
//decomposition. The two |
| 160 |
< |
//indices could be local or row |
| 161 |
< |
//& column. It will be up to |
| 162 |
< |
//the specific decomposition |
| 163 |
< |
//method to fill this. |
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< |
map<pair<int, int>, bool> exclude; //< exclude is the set of pairs |
| 164 |
< |
//to leave out of non-bonded |
| 165 |
< |
//force evaluations. This |
| 166 |
< |
//declaration is agnostic |
| 167 |
< |
//regarding the parallel |
| 168 |
< |
//decomposition. The two |
| 169 |
< |
//indices could be local or row |
| 170 |
< |
//& column. It will be up to |
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< |
//the specific decomposition |
| 172 |
< |
//method to fill this. |
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< |
|
| 154 |
> |
/** |
| 155 |
> |
* The topological distance between two atomic sites is handled |
| 156 |
> |
* via two vector structures for speed. These structures agnostic |
| 157 |
> |
* regarding the parallel decomposition. The index for |
| 158 |
> |
* toposForAtom could be local or row, while the values could be |
| 159 |
> |
* local or column. It will be up to the specific decomposition |
| 160 |
> |
* method to fill these. |
| 161 |
> |
*/ |
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> |
vector<vector<int> > toposForAtom; |
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> |
vector<vector<int> > topoDist; |
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> |
vector<vector<int> > skipsForAtom; |
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vector<vector<int> > groupList_; |
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+ |
vector<RealType> massFactors; |
| 167 |
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vector<Vector3i> cellOffsets_; |
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Vector3i nCells_; |
