| 1 |
/* |
| 2 |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
* documentation and/or other materials provided with the |
| 15 |
* distribution. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 28 |
* arising out of the use of or inability to use software, even if the |
| 29 |
* University of Notre Dame has been advised of the possibility of |
| 30 |
* such damages. |
| 31 |
* |
| 32 |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
* research, please cite the appropriate papers when you publish your |
| 34 |
* work. Good starting points are: |
| 35 |
* |
| 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). |
| 40 |
*/ |
| 41 |
|
| 42 |
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 43 |
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP |
| 44 |
|
| 45 |
#include "Parallel/ForceDecomposition.hpp" |
| 46 |
#include "math/SquareMatrix3.hpp" |
| 47 |
#include "brains/Snapshot.hpp" |
| 48 |
|
| 49 |
#ifdef IS_MPI |
| 50 |
#include "Parallel/Communicator.hpp" |
| 51 |
#endif |
| 52 |
|
| 53 |
using namespace std; |
| 54 |
namespace OpenMD { |
| 55 |
|
| 56 |
class ForceMatrixDecomposition : public ForceDecomposition { |
| 57 |
public: |
| 58 |
ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();} |
| 59 |
void distributeInitialData(); |
| 60 |
void distributeData(); |
| 61 |
void collectIntermediateData(); |
| 62 |
void distributeIntermediateData(); |
| 63 |
void collectData(); |
| 64 |
|
| 65 |
// neighbor list routines |
| 66 |
bool checkNeighborList(); |
| 67 |
vector<pair<int, int> > buildNeighborList(); |
| 68 |
|
| 69 |
// group bookkeeping |
| 70 |
pair<int, int> getGroupTypes(int cg1, int cg2); |
| 71 |
|
| 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 |
| 101 |
|
| 102 |
DataStorage atomRowData; |
| 103 |
DataStorage atomColData; |
| 104 |
DataStorage cgRowData; |
| 105 |
DataStorage cgColData; |
| 106 |
|
| 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> identsRow; |
| 125 |
vector<int> identsCol; |
| 126 |
|
| 127 |
vector<int> AtomLocalToGlobal; |
| 128 |
vector<int> AtomRowToGlobal; |
| 129 |
vector<int> AtomColToGlobal; |
| 130 |
vector<int> cgLocalToGlobal; |
| 131 |
vector<int> cgRowToGlobal; |
| 132 |
vector<int> cgColToGlobal; |
| 133 |
#endif |
| 134 |
vector<RealType> pot_local; |
| 135 |
}; |
| 136 |
|
| 137 |
} |
| 138 |
#endif |
| 139 |
|
