| 45 |
|
#include "brains/SimInfo.hpp" |
| 46 |
|
#include "brains/SnapshotManager.hpp" |
| 47 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 48 |
+ |
#include "nonbonded/Cutoffs.hpp" |
| 49 |
+ |
#include "nonbonded/InteractionManager.hpp" |
| 50 |
+ |
#include "utils/Tuple.hpp" |
| 51 |
|
|
| 52 |
|
using namespace std; |
| 53 |
|
namespace OpenMD { |
| 54 |
|
|
| 55 |
+ |
typedef tuple3<RealType, RealType, RealType> groupCutoffs; |
| 56 |
+ |
|
| 57 |
|
/** |
| 58 |
|
* @class ForceDecomposition |
| 59 |
|
* |
| 91 |
|
class ForceDecomposition { |
| 92 |
|
public: |
| 93 |
|
|
| 94 |
< |
ForceDecomposition(SimInfo* info); |
| 94 |
> |
ForceDecomposition(SimInfo* info, InteractionManager* iMan); |
| 95 |
|
virtual ~ForceDecomposition() {} |
| 96 |
|
|
| 97 |
|
virtual void distributeInitialData() = 0; |
| 98 |
|
virtual void distributeData() = 0; |
| 99 |
+ |
virtual void zeroWorkArrays() = 0; |
| 100 |
|
virtual void collectIntermediateData() = 0; |
| 101 |
|
virtual void distributeIntermediateData() = 0; |
| 102 |
|
virtual void collectData() = 0; |
| 103 |
+ |
virtual potVec getLongRangePotential() { return longRangePot_; } |
| 104 |
|
|
| 105 |
|
// neighbor list routines |
| 106 |
|
virtual bool checkNeighborList(); |
| 107 |
|
virtual vector<pair<int, int> > buildNeighborList() = 0; |
| 108 |
|
|
| 109 |
+ |
// how to handle cutoffs: |
| 110 |
+ |
void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;} |
| 111 |
+ |
void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; } |
| 112 |
+ |
|
| 113 |
|
// group bookkeeping |
| 114 |
< |
virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0; |
| 114 |
> |
virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0; |
| 115 |
|
|
| 116 |
|
// Group->atom bookkeeping |
| 117 |
|
virtual vector<int> getAtomsInGroupRow(int cg1) = 0; |
| 127 |
|
virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0; |
| 128 |
|
|
| 129 |
|
// atom bookkeeping |
| 130 |
< |
virtual vector<int> getAtomList() = 0; |
| 130 |
> |
virtual int getNAtomsInRow() = 0; |
| 131 |
|
virtual vector<int> getSkipsForAtom(int atom1) = 0; |
| 132 |
|
virtual bool skipAtomPair(int atom1, int atom2) = 0; |
| 133 |
|
virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0; |
| 134 |
|
virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0; |
| 135 |
+ |
virtual int getTopologicalDistance(int atom1, int atom2) = 0; |
| 136 |
|
|
| 137 |
|
// filling interaction blocks with pointers |
| 138 |
< |
virtual InteractionData fillInteractionData(int atom1, int atom2) = 0; |
| 139 |
< |
virtual InteractionData fillSkipData(int atom1, int atom2) = 0; |
| 140 |
< |
virtual SelfData fillSelfData(int atom1); |
| 138 |
> |
virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
| 139 |
> |
virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0; |
| 140 |
> |
virtual void fillSkipData(InteractionData &idat, int atom1, int atom2) = 0; |
| 141 |
> |
virtual void fillSelfData(SelfData &sdat, int atom1); |
| 142 |
|
|
| 143 |
|
protected: |
| 144 |
|
SimInfo* info_; |
| 145 |
|
SnapshotManager* sman_; |
| 146 |
|
Snapshot* snap_; |
| 147 |
+ |
ForceField* ff_; |
| 148 |
+ |
InteractionManager* interactionMan_; |
| 149 |
+ |
|
| 150 |
|
int storageLayout_; |
| 151 |
|
RealType skinThickness_; /**< Verlet neighbor list skin thickness */ |
| 152 |
+ |
RealType largestRcut_; |
| 153 |
|
|
| 154 |
< |
map<pair<int, int>, int> topoDist; //< topoDist gives the |
| 155 |
< |
//topological distance between |
| 156 |
< |
//two atomic sites. This |
| 157 |
< |
//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. |
| 164 |
< |
map<pair<int, int>, bool> exclude; //< exclude is the set of pairs |
| 148 |
< |
//to leave out of non-bonded |
| 149 |
< |
//force evaluations. This |
| 150 |
< |
//declaration is agnostic |
| 151 |
< |
//regarding the parallel |
| 152 |
< |
//decomposition. The two |
| 153 |
< |
//indices could be local or row |
| 154 |
< |
//& column. It will be up to |
| 155 |
< |
//the specific decomposition |
| 156 |
< |
//method to fill this. |
| 157 |
< |
|
| 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 |
> |
*/ |
| 162 |
> |
vector<vector<int> > toposForAtom; |
| 163 |
> |
vector<vector<int> > topoDist; |
| 164 |
> |
vector<vector<int> > skipsForAtom; |
| 165 |
|
vector<vector<int> > groupList_; |
| 166 |
+ |
vector<RealType> massFactors; |
| 167 |
+ |
|
| 168 |
|
vector<Vector3i> cellOffsets_; |
| 169 |
|
Vector3i nCells_; |
| 170 |
|
vector<vector<int> > cellList_; |
| 171 |
|
vector<Vector3d> saved_CG_positions_; |
| 172 |
+ |
potVec longRangePot_; |
| 173 |
|
|
| 174 |
+ |
bool userChoseCutoff_; |
| 175 |
+ |
RealType userCutoff_; |
| 176 |
+ |
CutoffPolicy cutoffPolicy_; |
| 177 |
+ |
|
| 178 |
+ |
map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap; |
| 179 |
+ |
|
| 180 |
|
}; |
| 181 |
|
} |
| 182 |
|
#endif |
