| 55 |
|
|
| 56 |
|
class ForceMatrixDecomposition : public ForceDecomposition { |
| 57 |
|
public: |
| 58 |
< |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {}; |
| 58 |
> |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
| 59 |
|
|
| 60 |
|
void distributeInitialData(); |
| 61 |
|
void zeroWorkArrays(); |
| 66 |
|
|
| 67 |
|
// neighbor list routines |
| 68 |
|
vector<pair<int, int> > buildNeighborList(); |
| 69 |
+ |
// neighbor list routines based on Rapaport |
| 70 |
+ |
vector<vector<int> > buildLayerBasedNeighborList(); |
| 71 |
|
|
| 72 |
|
// group bookkeeping |
| 73 |
|
groupCutoffs getGroupCutoffs(int cg1, int cg2); |
| 87 |
|
// atom bookkeeping |
| 88 |
|
int getNAtomsInRow(); |
| 89 |
|
int getTopologicalDistance(int atom1, int atom2); |
| 90 |
< |
vector<int> getSkipsForAtom(int atom1); |
| 90 |
> |
vector<int> getExcludesForAtom(int atom1); |
| 91 |
|
bool skipAtomPair(int atom1, int atom2); |
| 92 |
+ |
bool excludeAtomPair(int atom1, int atom2); |
| 93 |
|
void addForceToAtomRow(int atom1, Vector3d fg); |
| 94 |
|
void addForceToAtomColumn(int atom2, Vector3d fg); |
| 95 |
|
|
| 96 |
|
// filling interaction blocks with pointers |
| 97 |
< |
InteractionData fillInteractionData(int atom1, int atom2); |
| 98 |
< |
void unpackInteractionData(InteractionData idat, int atom1, int atom2); |
| 96 |
< |
InteractionData fillSkipData(int atom1, int atom2); |
| 97 |
> |
void fillInteractionData(InteractionData &idat, int atom1, int atom2); |
| 98 |
> |
void unpackInteractionData(InteractionData &idat, int atom1, int atom2); |
| 99 |
|
|
| 100 |
|
private: |
| 101 |
|
void createGtypeCutoffMap(); |
| 102 |
|
|
| 103 |
|
int nLocal_; |
| 104 |
|
int nGroups_; |
| 103 |
– |
vector<int> identsLocal; |
| 105 |
|
vector<int> AtomLocalToGlobal; |
| 106 |
|
vector<int> cgLocalToGlobal; |
| 106 |
– |
vector<RealType> massFactorsLocal; |
| 107 |
|
vector<RealType> groupCutoff; |
| 108 |
|
vector<int> groupToGtype; |
| 109 |
|
|
| 118 |
|
int nGroupsInRow_; |
| 119 |
|
int nGroupsInCol_; |
| 120 |
|
|
| 121 |
< |
Communicator<Row, int>* AtomCommIntRow; |
| 122 |
< |
Communicator<Row, RealType>* AtomCommRealRow; |
| 123 |
< |
Communicator<Row, Vector3d>* AtomCommVectorRow; |
| 124 |
< |
Communicator<Row, Mat3x3d>* AtomCommMatrixRow; |
| 125 |
< |
Communicator<Row, potVec>* AtomCommPotRow; |
| 121 |
> |
Communicator<Row> rowComm; |
| 122 |
> |
Communicator<Column> colComm; |
| 123 |
|
|
| 124 |
< |
Communicator<Column, int>* AtomCommIntColumn; |
| 125 |
< |
Communicator<Column, RealType>* AtomCommRealColumn; |
| 126 |
< |
Communicator<Column, Vector3d>* AtomCommVectorColumn; |
| 127 |
< |
Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
| 128 |
< |
Communicator<Column, potVec>* AtomCommPotColumn; |
| 124 |
> |
Plan<int>* AtomPlanIntRow; |
| 125 |
> |
Plan<RealType>* AtomPlanRealRow; |
| 126 |
> |
Plan<Vector3d>* AtomPlanVectorRow; |
| 127 |
> |
Plan<Mat3x3d>* AtomPlanMatrixRow; |
| 128 |
> |
Plan<potVec>* AtomPlanPotRow; |
| 129 |
|
|
| 130 |
< |
Communicator<Row, int>* cgCommIntRow; |
| 131 |
< |
Communicator<Row, Vector3d>* cgCommVectorRow; |
| 132 |
< |
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 |
|
|
| 136 |
+ |
Plan<int>* cgPlanIntRow; |
| 137 |
+ |
Plan<Vector3d>* cgPlanVectorRow; |
| 138 |
+ |
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; |
| 141 |
– |
potVec pot_local; |
| 144 |
|
|
| 145 |
|
vector<int> identsRow; |
| 146 |
|
vector<int> identsCol; |
