| 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). |
| 38 |
|
* [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_FORCEDECOMPOSITION_HPP |
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#define PARALLEL_FORCEDECOMPOSITION_HPP |
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|
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#include "brains/SimInfo.hpp" |
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+ |
#include "brains/SnapshotManager.hpp" |
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#include "nonbonded/NonBondedInteraction.hpp" |
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+ |
#include "nonbonded/Cutoffs.hpp" |
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#include "nonbonded/InteractionManager.hpp" |
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#include "utils/Tuple.hpp" |
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|
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using namespace std; |
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namespace OpenMD { |
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|
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+ |
typedef tuple3<RealType, RealType, RealType> groupCutoffs; |
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+ |
|
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/** |
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* @class ForceDecomposition |
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* |
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class ForceDecomposition { |
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public: |
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|
| 95 |
< |
ForceDecomposition(SimInfo* info); |
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> |
ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
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virtual ~ForceDecomposition() {} |
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|
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virtual void distributeInitialData() = 0; |
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virtual void distributeData() = 0; |
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+ |
virtual void zeroWorkArrays() = 0; |
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virtual void collectIntermediateData() = 0; |
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virtual void distributeIntermediateData() = 0; |
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virtual void collectData() = 0; |
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+ |
virtual potVec* getEmbeddingPotential() { return &embeddingPot; } |
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virtual potVec* getPairwisePotential() { return &pairwisePot; } |
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|
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// neighbor list routines |
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< |
virtual bool checkNeighborList() = 0; |
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> |
virtual bool checkNeighborList(); |
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virtual vector<pair<int, int> > buildNeighborList() = 0; |
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|
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+ |
// how to handle cutoffs: |
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void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
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void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
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|
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// group bookkeeping |
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< |
virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0; |
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> |
virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
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> |
virtual Vector3d getGroupVelocityColumn(int atom2) = 0; |
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|
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// Group->atom bookkeeping |
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< |
virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
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> |
virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
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virtual vector<int> getAtomsInGroupColumn(int cg2) = 0; |
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+ |
|
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virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0; |
| 124 |
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virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0; |
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< |
virtual RealType getMfactRow(int atom1) = 0; |
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< |
virtual RealType getMfactColumn(int atom2) = 0; |
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> |
virtual RealType getMassFactorRow(int atom1) = 0; |
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> |
virtual RealType getMassFactorColumn(int atom2) = 0; |
| 127 |
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|
| 128 |
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// spatial data |
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virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0; |
| 130 |
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virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; |
| 131 |
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|
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// atom bookkeeping |
| 133 |
< |
virtual vector<int> getAtomList() = 0; |
| 134 |
< |
virtual vector<int> getSkipsForAtom(int atom1) = 0; |
| 133 |
> |
virtual int getNAtomsInRow() = 0; |
| 134 |
> |
virtual vector<int> getExcludesForAtom(int atom1) = 0; |
| 135 |
|
virtual bool skipAtomPair(int atom1, int atom2) = 0; |
| 136 |
+ |
virtual bool excludeAtomPair(int atom1, int atom2) = 0; |
| 137 |
+ |
virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
| 138 |
|
virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
| 139 |
|
virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
| 140 |
+ |
virtual Vector3d getAtomVelocityColumn(int atom2) = 0; |
| 141 |
|
|
| 142 |
|
// filling interaction blocks with pointers |
| 143 |
< |
virtual InteractionData fillInteractionData(int atom1, int atom2) = 0; |
| 144 |
< |
virtual InteractionData fillSkipData(int atom1, int atom2) = 0; |
| 145 |
< |
virtual SelfData fillSelfData(int atom1) = 0; |
| 143 |
> |
virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
| 144 |
> |
virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
| 145 |
> |
|
| 146 |
> |
virtual void fillSelfData(SelfData &sdat, int atom1); |
| 147 |
> |
|
| 148 |
> |
virtual void addToHeatFlux(Vector3d hf); |
| 149 |
> |
virtual void setHeatFlux(Vector3d hf); |
| 150 |
|
|
| 151 |
|
protected: |
| 152 |
|
SimInfo* info_; |
| 153 |
< |
map<pair<int, int>, int> topoDist; //< topoDist gives the |
| 154 |
< |
//topological distance between |
| 155 |
< |
//two atomic sites. This |
| 156 |
< |
//declaration is agnostic |
| 157 |
< |
//regarding the parallel |
| 158 |
< |
//decomposition. The two |
| 159 |
< |
//indices could be local or row |
| 160 |
< |
//& column. It will be up to |
| 161 |
< |
//the specific decomposition |
| 162 |
< |
//method to fill this. |
| 163 |
< |
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 |
| 171 |
< |
//the specific decomposition |
| 172 |
< |
//method to fill this. |
| 153 |
> |
SnapshotManager* sman_; |
| 154 |
> |
Snapshot* snap_; |
| 155 |
> |
ForceField* ff_; |
| 156 |
> |
InteractionManager* interactionMan_; |
| 157 |
> |
|
| 158 |
> |
int storageLayout_; |
| 159 |
> |
bool needVelocities_; |
| 160 |
> |
RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
| 161 |
> |
RealType largestRcut_; |
| 162 |
> |
|
| 163 |
> |
vector<int> idents; |
| 164 |
> |
potVec pairwisePot; |
| 165 |
> |
potVec embeddingPot; |
| 166 |
> |
|
| 167 |
> |
/** |
| 168 |
> |
* The topological distance between two atomic sites is handled |
| 169 |
> |
* via two vector structures for speed. These structures agnostic |
| 170 |
> |
* regarding the parallel decomposition. The index for |
| 171 |
> |
* toposForAtom could be local or row, while the values could be |
| 172 |
> |
* local or column. It will be up to the specific decomposition |
| 173 |
> |
* method to fill these. |
| 174 |
> |
*/ |
| 175 |
> |
vector<vector<int> > toposForAtom; |
| 176 |
> |
vector<vector<int> > topoDist; |
| 177 |
> |
vector<vector<int> > excludesForAtom; |
| 178 |
> |
vector<vector<int> > groupList_; |
| 179 |
> |
vector<RealType> massFactors; |
| 180 |
> |
vector<AtomType*> atypesLocal; |
| 181 |
> |
|
| 182 |
|
vector<Vector3i> cellOffsets_; |
| 183 |
< |
int nOffset_; |
| 183 |
> |
Vector3i nCells_; |
| 184 |
> |
vector<vector<int> > cellList_; |
| 185 |
> |
vector<Vector3d> saved_CG_positions_; |
| 186 |
> |
|
| 187 |
> |
bool userChoseCutoff_; |
| 188 |
> |
RealType userCutoff_; |
| 189 |
> |
CutoffPolicy cutoffPolicy_; |
| 190 |
> |
|
| 191 |
> |
map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
| 192 |
> |
|
| 193 |
|
}; |
| 194 |
|
} |
| 195 |
|
#endif |
