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
File size:	5378 byte(s)
Log Message:	Fixed some busted stuff in buildNeighborList
#	Content
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	vector<Vector3i> Cells;
101
102	int nLocal_;
103	int nGroups_;
104
105	#ifdef IS_MPI
106	DataStorage atomRowData;
107	DataStorage atomColData;
108	DataStorage cgRowData;
109	DataStorage cgColData;
110
111	int nAtomsInRow_;
112	int nAtomsInCol_;
113	int nGroupsInRow_;
114	int nGroupsInCol_;
115
116	Communicator<Row, int>* AtomCommIntRow;
117	Communicator<Row, RealType>* AtomCommRealRow;
118	Communicator<Row, Vector3d>* AtomCommVectorRow;
119	Communicator<Row, Mat3x3d>* AtomCommMatrixRow;
120
121	Communicator<Column, int>* AtomCommIntColumn;
122	Communicator<Column, RealType>* AtomCommRealColumn;
123	Communicator<Column, Vector3d>* AtomCommVectorColumn;
124	Communicator<Column, Mat3x3d>* AtomCommMatrixColumn;
125
126	Communicator<Row, int>* cgCommIntRow;
127	Communicator<Row, Vector3d>* cgCommVectorRow;
128	Communicator<Column, int>* cgCommIntColumn;
129	Communicator<Column, Vector3d>* cgCommVectorColumn;
130
131	vector<vector<RealType> > pot_row;
132	vector<vector<RealType> > pot_col;
133	vector<int> identsRow;
134	vector<int> identsCol;
135
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
143	vector<vector<int> > CellListRow;
144	vector<vector<int> > CellListCol;
145	#else
146	vector<vector<int> > CellList;
147	#endif
148	vector<RealType> pot_local;
149
150	};
151
152	}
153	#endif
154