| 39 |
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* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
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*/ |
| 41 |
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|
| 42 |
< |
#ifndef PARALLEL_FORCEDECOMPOSITION_HPP |
| 43 |
< |
#define PARALLEL_FORCEDECOMPOSITION_HPP |
| 42 |
> |
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 43 |
> |
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 44 |
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|
| 45 |
< |
#include "Parallel/Decomposition.hpp" |
| 45 |
> |
#include "Parallel/ForceDecomposition.hpp" |
| 46 |
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#include "math/SquareMatrix3.hpp" |
| 47 |
+ |
#include "brains/Snapshot.hpp" |
| 48 |
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|
| 49 |
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#ifdef IS_MPI |
| 50 |
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#include "Parallel/Communicator.hpp" |
| 53 |
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using namespace std; |
| 54 |
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namespace OpenMD { |
| 55 |
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|
| 56 |
< |
class ForceDecomposition : public Decomposition { |
| 56 |
> |
class ForceMatrixDecomposition : public ForceDecomposition { |
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public: |
| 58 |
< |
ForceDecomposition(SimInfo* info) : Decomposition(info) {sman_ = info_->getSnapshotManager();} |
| 58 |
> |
ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();} |
| 59 |
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void distributeInitialData(); |
| 60 |
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void distributeData(); |
| 61 |
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void collectIntermediateData(); |
| 62 |
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void distributeIntermediateData(); |
| 63 |
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void collectData(); |
| 64 |
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|
| 65 |
< |
unsigned int getNcutoffGroupsI(); |
| 66 |
< |
unsigned int getNcutoffGroupsJ(); |
| 65 |
> |
// neighbor list routines |
| 66 |
> |
bool checkNeighborList(); |
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> |
vector<pair<int, int> > buildNeighborList(); |
| 68 |
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|
| 69 |
< |
vector<int> getAtomsInGroupI(int whichCGI); |
| 70 |
< |
vector<int> getAtomsInGroupJ(int whichCGJ); |
| 69 |
> |
// group bookkeeping |
| 70 |
> |
pair<int, int> getGroupTypes(int cg1, int cg2); |
| 71 |
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|
| 72 |
< |
AtomType* getAtomTypeI(int whichAtomI); |
| 73 |
< |
AtomType* getAtomTypeJ(int whichAtomJ); |
| 72 |
> |
// Group->atom bookkeeping |
| 73 |
> |
vector<int> getAtomsInGroupRow(int cg1); |
| 74 |
> |
vector<int> getAtomsInGroupColumn(int cg2); |
| 75 |
> |
Vector3d getAtomToGroupVectorRow(int atom1, int cg1); |
| 76 |
> |
Vector3d getAtomToGroupVectorColumn(int atom2, int cg2); |
| 77 |
> |
RealType getMfactRow(int atom1); |
| 78 |
> |
RealType getMfactColumn(int atom2); |
| 79 |
|
|
| 80 |
+ |
// spatial data |
| 81 |
+ |
Vector3d getIntergroupVector(int cg1, int cg2); |
| 82 |
+ |
Vector3d getInteratomicVector(int atom1, int atom2); |
| 83 |
+ |
|
| 84 |
+ |
// atom bookkeeping |
| 85 |
+ |
vector<int> getAtomList(); |
| 86 |
+ |
vector<int> getSkipsForAtom(int atom1); |
| 87 |
+ |
bool skipAtomPair(int atom1, int atom2); |
| 88 |
+ |
void addForceToAtomRow(int atom1, Vector3d fg); |
| 89 |
+ |
void addForceToAtomColumn(int atom2, Vector3d fg); |
| 90 |
+ |
|
| 91 |
+ |
// filling interaction blocks with pointers |
| 92 |
+ |
InteractionData fillInteractionData(int atom1, int atom2); |
| 93 |
+ |
InteractionData fillSkipData(int atom1, int atom2); |
| 94 |
+ |
SelfData fillSelfData(int atom1); |
| 95 |
+ |
|
| 96 |
|
private: |
| 97 |
|
SnapshotManager* sman_; |
| 98 |
+ |
Snapshot* snap_; |
| 99 |
+ |
int storageLayout_; |
| 100 |
|
#ifdef IS_MPI |
| 76 |
– |
Communicator<Row, int>* AtomCommIntI; |
| 77 |
– |
Communicator<Row, RealType>* AtomCommRealI; |
| 78 |
– |
Communicator<Row, Vector3d>* AtomCommVectorI; |
| 79 |
– |
Communicator<Row, Mat3x3d>* AtomCommMatrixI; |
| 101 |
|
|
| 102 |
< |
Communicator<Column, int>* AtomCommIntJ; |
| 103 |
< |
Communicator<Column, RealType>* AtomCommRealJ; |
| 104 |
< |
Communicator<Column, Vector3d>* AtomCommVectorJ; |
| 105 |
< |
Communicator<Column, Mat3x3d>* AtomCommMatrixJ; |
| 102 |
> |
DataStorage atomRowData; |
| 103 |
> |
DataStorage atomColData; |
| 104 |
> |
DataStorage cgRowData; |
| 105 |
> |
DataStorage cgColData; |
| 106 |
|
|
| 107 |
< |
Communicator<Row, int>* cgCommIntI; |
| 108 |
< |
Communicator<Row, Vector3d>* cgCommVectorI; |
| 109 |
< |
Communicator<Column, int>* cgCommIntJ; |
| 110 |
< |
Communicator<Column, Vector3d>* cgCommVectorJ; |
| 107 |
> |
Communicator<Row, int>* AtomCommIntRow; |
| 108 |
> |
Communicator<Row, RealType>* AtomCommRealRow; |
| 109 |
> |
Communicator<Row, Vector3d>* AtomCommVectorRow; |
| 110 |
> |
Communicator<Row, Mat3x3d>* AtomCommMatrixRow; |
| 111 |
|
|
| 112 |
+ |
Communicator<Column, int>* AtomCommIntColumn; |
| 113 |
+ |
Communicator<Column, RealType>* AtomCommRealColumn; |
| 114 |
+ |
Communicator<Column, Vector3d>* AtomCommVectorColumn; |
| 115 |
+ |
Communicator<Column, Mat3x3d>* AtomCommMatrixColumn; |
| 116 |
+ |
|
| 117 |
+ |
Communicator<Row, int>* cgCommIntRow; |
| 118 |
+ |
Communicator<Row, Vector3d>* cgCommVectorRow; |
| 119 |
+ |
Communicator<Column, int>* cgCommIntColumn; |
| 120 |
+ |
Communicator<Column, Vector3d>* cgCommVectorColumn; |
| 121 |
+ |
|
| 122 |
|
vector<vector<RealType> > pot_row; |
| 123 |
|
vector<vector<RealType> > pot_col; |
| 124 |
< |
vector<int> identRow; |
| 125 |
< |
vector<int> identCol; |
| 124 |
> |
vector<int> identsRow; |
| 125 |
> |
vector<int> identsCol; |
| 126 |
|
|
| 127 |
|
vector<int> AtomLocalToGlobal; |
| 128 |
|
vector<int> AtomRowToGlobal; |
