src/parallel/ForceMatrixDecomposition.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP

#include "parallel/ForceDecomposition.hpp"
#include "math/SquareMatrix3.hpp"
#include "brains/Snapshot.hpp"

#ifdef IS_MPI
#include "parallel/Communicator.hpp"
#endif

using namespace std;
namespace OpenMD {
  
  class ForceMatrixDecomposition : public ForceDecomposition {
  public:
    ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
    void distributeInitialData();
    void distributeData();
    void collectIntermediateData();
    void distributeIntermediateData();
    void collectData();

    // neighbor list routines
    bool checkNeighborList();
    vector<pair<int, int> >  buildNeighborList();

    // group bookkeeping
    pair<int, int> getGroupTypes(int cg1, int cg2);

    // Group->atom bookkeeping
    vector<int> getAtomsInGroupRow(int cg1);
    vector<int> getAtomsInGroupColumn(int cg2);
    Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
    Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
    RealType getMfactRow(int atom1);
    RealType getMfactColumn(int atom2);

    // spatial data
    Vector3d getIntergroupVector(int cg1, int cg2);
    Vector3d getInteratomicVector(int atom1, int atom2);
       
    // atom bookkeeping
    vector<int> getAtomList();
    vector<int> getSkipsForAtom(int atom1);
    bool skipAtomPair(int atom1, int atom2);
    void addForceToAtomRow(int atom1, Vector3d fg);
    void addForceToAtomColumn(int atom2, Vector3d fg);

    // filling interaction blocks with pointers
    InteractionData fillInteractionData(int atom1, int atom2);
    InteractionData fillSkipData(int atom1, int atom2);
    SelfData fillSelfData(int atom1);

  private: 
    SnapshotManager* sman_;    
    Snapshot* snap_;
    int storageLayout_;
    vector<Vector3i> Cells;

    int nLocal_;
    int nGroups_;

#ifdef IS_MPI    
    DataStorage atomRowData;
    DataStorage atomColData;
    DataStorage cgRowData;
    DataStorage cgColData;

    int nAtomsInRow_; 
    int nAtomsInCol_;
    int nGroupsInRow_;
    int nGroupsInCol_;

    Communicator<Row, int>* AtomCommIntRow;
    Communicator<Row, RealType>* AtomCommRealRow; 
    Communicator<Row, Vector3d>* AtomCommVectorRow; 
    Communicator<Row, Mat3x3d>*  AtomCommMatrixRow; 

    Communicator<Column, int>* AtomCommIntColumn;
    Communicator<Column, RealType>* AtomCommRealColumn; 
    Communicator<Column, Vector3d>* AtomCommVectorColumn; 
    Communicator<Column, Mat3x3d>*  AtomCommMatrixColumn; 

    Communicator<Row, int>* cgCommIntRow;
    Communicator<Row, Vector3d>* cgCommVectorRow; 
    Communicator<Column, int>* cgCommIntColumn;
    Communicator<Column, Vector3d>* cgCommVectorColumn; 

    vector<vector<RealType> > pot_row;
    vector<vector<RealType> > pot_col;
    vector<int> identsRow;
    vector<int> identsCol;

    vector<int> AtomLocalToGlobal;
    vector<int> AtomRowToGlobal;
    vector<int> AtomColToGlobal;
    vector<int> cgLocalToGlobal;
    vector<int> cgRowToGlobal;
    vector<int> cgColToGlobal;

    vector<vector<int> > CellListRow;
    vector<vector<int> > CellListCol;
#else 
    vector<vector<int> > CellList;
#endif
    vector<RealType> pot_local;

  };

}
#endif

Revision:	1567
Committed:	Tue May 24 21:24:45 2011 UTC (13 years, 11 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceMatrixDecomposition.hpp*
File size:	5378 byte(s)
Log Message:	Fixed some busted stuff in buildNeighborList
#	User	Rev	Content
1	gezelter	1539	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	chuckv	1538	*
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	gezelter	1539
42	gezelter	1549	#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
43			#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44	chuckv	1538
45	gezelter	1567	#include "parallel/ForceDecomposition.hpp"
46	gezelter	1539	#include "math/SquareMatrix3.hpp"
47	gezelter	1551	#include "brains/Snapshot.hpp"
48	chuckv	1538
49	gezelter	1544	#ifdef IS_MPI
50	gezelter	1567	#include "parallel/Communicator.hpp"
51	gezelter	1544	#endif
52
53	gezelter	1541	using namespace std;
54	gezelter	1539	namespace OpenMD {
55	chuckv	1538
56	gezelter	1549	class ForceMatrixDecomposition : public ForceDecomposition {
57	gezelter	1539	public:
58	gezelter	1549	ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
59	gezelter	1539	void distributeInitialData();
60			void distributeData();
61			void collectIntermediateData();
62			void distributeIntermediateData();
63			void collectData();
64	chuckv	1538
65	gezelter	1549	// neighbor list routines
66			bool checkNeighborList();
67			vector<pair<int, int> > buildNeighborList();
68	chuckv	1538
69	gezelter	1549	// group bookkeeping
70			pair<int, int> getGroupTypes(int cg1, int cg2);
71	chuckv	1538
72	gezelter	1549	// 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	chuckv	1538
80	gezelter	1549	// 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	gezelter	1544	private:
97			SnapshotManager* sman_;
98	gezelter	1551	Snapshot* snap_;
99			int storageLayout_;
100	gezelter	1567	vector<Vector3i> Cells;
101
102			int nLocal_;
103			int nGroups_;
104
105	gezelter	1544	#ifdef IS_MPI
106	gezelter	1551	DataStorage atomRowData;
107			DataStorage atomColData;
108			DataStorage cgRowData;
109			DataStorage cgColData;
110
111	gezelter	1567	int nAtomsInRow_;
112			int nAtomsInCol_;
113			int nGroupsInRow_;
114			int nGroupsInCol_;
115
116	gezelter	1549	Communicator<Row, int>* AtomCommIntRow;
117			Communicator<Row, RealType>* AtomCommRealRow;
118			Communicator<Row, Vector3d>* AtomCommVectorRow;
119			Communicator<Row, Mat3x3d>* AtomCommMatrixRow;
120	chuckv	1538
121	gezelter	1549	Communicator<Column, int>* AtomCommIntColumn;
122			Communicator<Column, RealType>* AtomCommRealColumn;
123			Communicator<Column, Vector3d>* AtomCommVectorColumn;
124			Communicator<Column, Mat3x3d>* AtomCommMatrixColumn;
125	chuckv	1538
126	gezelter	1549	Communicator<Row, int>* cgCommIntRow;
127			Communicator<Row, Vector3d>* cgCommVectorRow;
128			Communicator<Column, int>* cgCommIntColumn;
129			Communicator<Column, Vector3d>* cgCommVectorColumn;
130	gezelter	1541
131			vector<vector<RealType> > pot_row;
132			vector<vector<RealType> > pot_col;
133	gezelter	1547	vector<int> identsRow;
134			vector<int> identsCol;
135	gezelter	1544
136			vector<int> AtomLocalToGlobal;
137			vector<int> AtomRowToGlobal;
138			vector<int> AtomColToGlobal;
139			vector<int> cgLocalToGlobal;
140			vector<int> cgRowToGlobal;
141			vector<int> cgColToGlobal;
142	gezelter	1567
143			vector<vector<int> > CellListRow;
144			vector<vector<int> > CellListCol;
145			#else
146			vector<vector<int> > CellList;
147	gezelter	1539	#endif
148	gezelter	1544	vector<RealType> pot_local;
149	gezelter	1567
150	gezelter	1539	};
151	chuckv	1538
152	gezelter	1539	}
153	chuckv	1538	#endif
154