| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
|
* [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 |
< |
#ifndef PARALLEL_FORCEDECOMPOSITION_HPP |
| 44 |
< |
#define PARALLEL_FORCEDECOMPOSITION_HPP |
| 43 |
> |
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 44 |
> |
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 45 |
|
|
| 46 |
< |
#include "Parallel/Decomposition.hpp" |
| 46 |
> |
#include "parallel/ForceDecomposition.hpp" |
| 47 |
|
#include "math/SquareMatrix3.hpp" |
| 48 |
+ |
#include "brains/Snapshot.hpp" |
| 49 |
|
|
| 50 |
|
#ifdef IS_MPI |
| 51 |
< |
#include "Parallel/Communicator.hpp" |
| 51 |
> |
#include "parallel/Communicator.hpp" |
| 52 |
|
#endif |
| 53 |
|
|
| 54 |
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using namespace std; |
| 55 |
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namespace OpenMD { |
| 56 |
|
|
| 57 |
< |
class ForceDecomposition : public Decomposition { |
| 57 |
> |
class ForceMatrixDecomposition : public ForceDecomposition { |
| 58 |
|
public: |
| 59 |
< |
ForceDecomposition(SimInfo* info) : Decomposition(info) {sman_ = info_->getSnapshotManager();} |
| 59 |
> |
ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan); |
| 60 |
> |
|
| 61 |
|
void distributeInitialData(); |
| 62 |
+ |
void zeroWorkArrays(); |
| 63 |
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void distributeData(); |
| 64 |
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void collectIntermediateData(); |
| 65 |
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void distributeIntermediateData(); |
| 66 |
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void collectData(); |
| 67 |
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|
| 68 |
< |
unsigned int getNcutoffGroupsI(); |
| 69 |
< |
unsigned int getNcutoffGroupsJ(); |
| 68 |
> |
// neighbor list routines |
| 69 |
> |
vector<pair<int, int> > buildNeighborList(); |
| 70 |
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|
| 71 |
< |
vector<int> getAtomsInGroupI(int whichCGI); |
| 72 |
< |
vector<int> getAtomsInGroupJ(int whichCGJ); |
| 71 |
> |
// group bookkeeping |
| 72 |
> |
groupCutoffs getGroupCutoffs(int cg1, int cg2); |
| 73 |
> |
Vector3d getGroupVelocityColumn(int cg2); |
| 74 |
|
|
| 75 |
< |
AtomType* getAtomTypeI(int whichAtomI); |
| 76 |
< |
AtomType* getAtomTypeJ(int whichAtomJ); |
| 75 |
> |
// Group->atom bookkeeping |
| 76 |
> |
vector<int> getAtomsInGroupRow(int cg1); |
| 77 |
> |
vector<int> getAtomsInGroupColumn(int cg2); |
| 78 |
> |
Vector3d getAtomToGroupVectorRow(int atom1, int cg1); |
| 79 |
> |
Vector3d getAtomToGroupVectorColumn(int atom2, int cg2); |
| 80 |
> |
RealType getMassFactorRow(int atom1); |
| 81 |
> |
RealType getMassFactorColumn(int atom2); |
| 82 |
|
|
| 83 |
+ |
// spatial data |
| 84 |
+ |
Vector3d getIntergroupVector(int cg1, int cg2); |
| 85 |
+ |
Vector3d getInteratomicVector(int atom1, int atom2); |
| 86 |
+ |
|
| 87 |
+ |
// atom bookkeeping |
| 88 |
+ |
int getNAtomsInRow(); |
| 89 |
+ |
int getTopologicalDistance(int atom1, int atom2); |
| 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 |
+ |
Vector3d getAtomVelocityColumn(int atom2); |
| 96 |
+ |
|
| 97 |
+ |
// filling interaction blocks with pointers |
| 98 |
+ |
void fillInteractionData(InteractionData &idat, int atom1, int atom2); |
| 99 |
+ |
void unpackInteractionData(InteractionData &idat, int atom1, int atom2); |
| 100 |
+ |
|
| 101 |
|
private: |
| 102 |
< |
SnapshotManager* sman_; |
| 102 |
> |
void createGtypeCutoffMap(); |
| 103 |
> |
|
| 104 |
> |
int nLocal_; |
| 105 |
> |
int nGroups_; |
| 106 |
> |
vector<int> AtomLocalToGlobal; |
| 107 |
> |
vector<int> cgLocalToGlobal; |
| 108 |
> |
vector<RealType> groupCutoff; |
| 109 |
> |
vector<int> groupToGtype; |
| 110 |
> |
|
| 111 |
|
#ifdef IS_MPI |
| 112 |
< |
Communicator<Row, int>* AtomCommIntI; |
| 113 |
< |
Communicator<Row, RealType>* AtomCommRealI; |
| 114 |
< |
Communicator<Row, Vector3d>* AtomCommVectorI; |
| 79 |
< |
Communicator<Row, Mat3x3d>* AtomCommMatrixI; |
| 112 |
> |
DataStorage atomRowData; DataStorage atomColData; |
| 113 |
> |
DataStorage cgRowData; |
| 114 |
> |
DataStorage cgColData; |
| 115 |
|
|
| 116 |
< |
Communicator<Column, int>* AtomCommIntJ; |
| 117 |
< |
Communicator<Column, RealType>* AtomCommRealJ; |
| 118 |
< |
Communicator<Column, Vector3d>* AtomCommVectorJ; |
| 119 |
< |
Communicator<Column, Mat3x3d>* AtomCommMatrixJ; |
| 116 |
> |
int nAtomsInRow_; |
| 117 |
> |
int nAtomsInCol_; |
| 118 |
> |
int nGroupsInRow_; |
| 119 |
> |
int nGroupsInCol_; |
| 120 |
|
|
| 121 |
< |
Communicator<Row, int>* cgCommIntI; |
| 122 |
< |
Communicator<Row, Vector3d>* cgCommVectorI; |
| 88 |
< |
Communicator<Column, int>* cgCommIntJ; |
| 89 |
< |
Communicator<Column, Vector3d>* cgCommVectorJ; |
| 121 |
> |
Communicator<Row> rowComm; |
| 122 |
> |
Communicator<Column> colComm; |
| 123 |
|
|
| 124 |
< |
vector<vector<RealType> > pot_row; |
| 125 |
< |
vector<vector<RealType> > pot_col; |
| 126 |
< |
vector<int> identRow; |
| 127 |
< |
vector<int> identCol; |
| 124 |
> |
Plan<int>* AtomPlanIntRow; |
| 125 |
> |
Plan<RealType>* AtomPlanRealRow; |
| 126 |
> |
Plan<Vector3d>* AtomPlanVectorRow; |
| 127 |
> |
Plan<Mat3x3d>* AtomPlanMatrixRow; |
| 128 |
> |
Plan<potVec>* AtomPlanPotRow; |
| 129 |
|
|
| 130 |
< |
vector<int> AtomLocalToGlobal; |
| 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; |
| 144 |
> |
|
| 145 |
> |
vector<int> identsRow; |
| 146 |
> |
vector<int> identsCol; |
| 147 |
> |
|
| 148 |
> |
vector<AtomType*> atypesRow; |
| 149 |
> |
vector<AtomType*> atypesCol; |
| 150 |
> |
|
| 151 |
|
vector<int> AtomRowToGlobal; |
| 152 |
|
vector<int> AtomColToGlobal; |
| 153 |
< |
vector<int> cgLocalToGlobal; |
| 153 |
> |
|
| 154 |
> |
public: |
| 155 |
|
vector<int> cgRowToGlobal; |
| 156 |
|
vector<int> cgColToGlobal; |
| 157 |
+ |
|
| 158 |
+ |
private: |
| 159 |
+ |
vector<RealType> groupCutoffRow; |
| 160 |
+ |
vector<RealType> groupCutoffCol; |
| 161 |
+ |
vector<int> groupColToGtype; |
| 162 |
+ |
vector<int> groupRowToGtype; |
| 163 |
+ |
|
| 164 |
+ |
vector<vector<int> > cellListRow_; |
| 165 |
+ |
vector<vector<int> > cellListCol_; |
| 166 |
+ |
|
| 167 |
+ |
vector<vector<int> > groupListRow_; |
| 168 |
+ |
vector<vector<int> > groupListCol_; |
| 169 |
+ |
|
| 170 |
+ |
vector<RealType> massFactorsRow; |
| 171 |
+ |
vector<RealType> massFactorsCol; |
| 172 |
|
#endif |
| 173 |
< |
vector<RealType> pot_local; |
| 173 |
> |
|
| 174 |
|
}; |
| 175 |
|
|
| 176 |
|
} |
