| 113 |
|
|
| 114 |
|
// neighbor list routines |
| 115 |
|
virtual bool checkNeighborList(); |
| 116 |
< |
virtual vector<pair<int, int> > buildNeighborList() = 0; |
| 116 |
> |
virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0; |
| 117 |
|
|
| 118 |
|
// how to handle cutoffs: |
| 119 |
|
void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
| 120 |
|
void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
| 121 |
|
|
| 122 |
|
// group bookkeeping |
| 123 |
< |
virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
| 124 |
< |
virtual Vector3d getGroupVelocityColumn(int atom2) = 0; |
| 123 |
> |
virtual void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) = 0; |
| 124 |
> |
virtual Vector3d& getGroupVelocityColumn(int atom2) = 0; |
| 125 |
|
|
| 126 |
|
// Group->atom bookkeeping |
| 127 |
< |
virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
| 128 |
< |
virtual vector<int> getAtomsInGroupColumn(int cg2) = 0; |
| 127 |
> |
virtual vector<int>& getAtomsInGroupRow(int cg1) = 0; |
| 128 |
> |
virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0; |
| 129 |
|
|
| 130 |
|
virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0; |
| 131 |
|
virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0; |
| 132 |
< |
virtual RealType getMassFactorRow(int atom1) = 0; |
| 133 |
< |
virtual RealType getMassFactorColumn(int atom2) = 0; |
| 132 |
> |
virtual RealType& getMassFactorRow(int atom1) = 0; |
| 133 |
> |
virtual RealType& getMassFactorColumn(int atom2) = 0; |
| 134 |
|
|
| 135 |
|
// spatial data |
| 136 |
|
virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0; |
| 137 |
|
virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; |
| 138 |
|
|
| 139 |
|
// atom bookkeeping |
| 140 |
< |
virtual int getNAtomsInRow() = 0; |
| 141 |
< |
virtual vector<int> getExcludesForAtom(int atom1) = 0; |
| 140 |
> |
virtual int& getNAtomsInRow() = 0; |
| 141 |
> |
virtual vector<int>& getExcludesForAtom(int atom1) = 0; |
| 142 |
|
virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0; |
| 143 |
|
virtual bool excludeAtomPair(int atom1, int atom2) = 0; |
| 144 |
|
virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
| 145 |
|
virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
| 146 |
|
virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
| 147 |
< |
virtual Vector3d getAtomVelocityColumn(int atom2) = 0; |
| 147 |
> |
virtual Vector3d& getAtomVelocityColumn(int atom2) = 0; |
| 148 |
|
|
| 149 |
|
// filling interaction blocks with pointers |
| 150 |
|
virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
| 169 |
|
RealType largestRcut_; |
| 170 |
|
|
| 171 |
|
vector<int> idents; |
| 172 |
+ |
vector<int> regions; |
| 173 |
|
potVec pairwisePot; |
| 174 |
|
potVec embeddingPot; |
| 175 |
|
potVec excludedPot; |
| 199 |
|
RealType userCutoff_; |
| 200 |
|
CutoffPolicy cutoffPolicy_; |
| 201 |
|
|
| 202 |
< |
map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
| 202 |
> |
//map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
| 203 |
> |
vector<vector<RealType> > GrCut; |
| 204 |
> |
vector<vector<RealType> > GrCutSq; |
| 205 |
> |
vector<vector<RealType> > GrlistSq; |
| 206 |
|
|
| 207 |
|
}; |
| 208 |
|
} |
