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, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};

    void distributeInitialData();
    void zeroWorkArrays();
    void distributeData();
    void collectIntermediateData();
    void distributeIntermediateData();
    void collectData();

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

    // group bookkeeping
    groupCutoffs getGroupCutoffs(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 getMassFactorRow(int atom1);
    RealType getMassFactorColumn(int atom2);

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

    // filling interaction blocks with pointers
    void fillInteractionData(InteractionData &idat, int atom1, int atom2);
    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);

  private: 
    void createGtypeCutoffMap();

    int nLocal_;
    int nGroups_;
    vector<int> AtomLocalToGlobal;
    vector<int> cgLocalToGlobal;
    vector<RealType> groupCutoff;
    vector<int> groupToGtype;

#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<Row, potVec>* AtomCommPotRow;

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

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

    // work arrays for assembling potential energy
    vector<potVec> pot_row;
    vector<potVec> pot_col;

    vector<int> identsRow;
    vector<int> identsCol;

    vector<AtomType*> atypesRow;
    vector<AtomType*> atypesCol;

    vector<int> AtomRowToGlobal;
    vector<int> AtomColToGlobal;

    vector<int> cgRowToGlobal;
    vector<int> cgColToGlobal;

    vector<RealType> groupCutoffRow;
    vector<RealType> groupCutoffCol;
    vector<int> groupColToGtype;
    vector<int> groupRowToGtype;

    vector<vector<int> > cellListRow_;
    vector<vector<int> > cellListCol_;

    vector<vector<int> > groupListRow_;
    vector<vector<int> > groupListCol_;

    vector<RealType> massFactorsRow;
    vector<RealType> massFactorsCol;
#endif

  };

}
#endif

Revision:	1587
Committed:	Fri Jul 8 20:25:32 2011 UTC (13 years, 9 months ago) by gezelter
File size:	5894 byte(s)
Log Message:	Fixes
#	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	1579	ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan) : ForceDecomposition(info, iMan) {};
59	gezelter	1568
60	gezelter	1539	void distributeInitialData();
61	gezelter	1575	void zeroWorkArrays();
62	gezelter	1539	void distributeData();
63			void collectIntermediateData();
64			void distributeIntermediateData();
65			void collectData();
66	chuckv	1538
67	gezelter	1549	// neighbor list routines
68			vector<pair<int, int> > buildNeighborList();
69	chuckv	1538
70	gezelter	1549	// group bookkeeping
71	gezelter	1576	groupCutoffs getGroupCutoffs(int cg1, int cg2);
72	chuckv	1538
73	gezelter	1549	// Group->atom bookkeeping
74			vector<int> getAtomsInGroupRow(int cg1);
75			vector<int> getAtomsInGroupColumn(int cg2);
76			Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
77			Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
78	gezelter	1569	RealType getMassFactorRow(int atom1);
79			RealType getMassFactorColumn(int atom2);
80	chuckv	1538
81	gezelter	1549	// spatial data
82			Vector3d getIntergroupVector(int cg1, int cg2);
83			Vector3d getInteratomicVector(int atom1, int atom2);
84
85			// atom bookkeeping
86	gezelter	1570	int getNAtomsInRow();
87	gezelter	1579	int getTopologicalDistance(int atom1, int atom2);
88	gezelter	1587	vector<int> getExcludesForAtom(int atom1);
89	gezelter	1549	bool skipAtomPair(int atom1, int atom2);
90	gezelter	1587	bool excludeAtomPair(int atom1, int atom2);
91	gezelter	1549	void addForceToAtomRow(int atom1, Vector3d fg);
92			void addForceToAtomColumn(int atom2, Vector3d fg);
93
94			// filling interaction blocks with pointers
95	gezelter	1582	void fillInteractionData(InteractionData &idat, int atom1, int atom2);
96			void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
97	gezelter	1549
98	gezelter	1544	private:
99	gezelter	1576	void createGtypeCutoffMap();
100
101	gezelter	1567	int nLocal_;
102			int nGroups_;
103	gezelter	1569	vector<int> AtomLocalToGlobal;
104			vector<int> cgLocalToGlobal;
105	gezelter	1576	vector<RealType> groupCutoff;
106			vector<int> groupToGtype;
107	gezelter	1567
108	gezelter	1544	#ifdef IS_MPI
109	gezelter	1551	DataStorage atomRowData;
110			DataStorage atomColData;
111			DataStorage cgRowData;
112			DataStorage cgColData;
113
114	gezelter	1567	int nAtomsInRow_;
115			int nAtomsInCol_;
116			int nGroupsInRow_;
117			int nGroupsInCol_;
118
119	gezelter	1549	Communicator<Row, int>* AtomCommIntRow;
120			Communicator<Row, RealType>* AtomCommRealRow;
121			Communicator<Row, Vector3d>* AtomCommVectorRow;
122			Communicator<Row, Mat3x3d>* AtomCommMatrixRow;
123	gezelter	1575	Communicator<Row, potVec>* AtomCommPotRow;
124	chuckv	1538
125	gezelter	1549	Communicator<Column, int>* AtomCommIntColumn;
126			Communicator<Column, RealType>* AtomCommRealColumn;
127			Communicator<Column, Vector3d>* AtomCommVectorColumn;
128	gezelter	1575	Communicator<Column, Mat3x3d>* AtomCommMatrixColumn;
129			Communicator<Column, potVec>* AtomCommPotColumn;
130	chuckv	1538
131	gezelter	1549	Communicator<Row, int>* cgCommIntRow;
132			Communicator<Row, Vector3d>* cgCommVectorRow;
133			Communicator<Column, int>* cgCommIntColumn;
134			Communicator<Column, Vector3d>* cgCommVectorColumn;
135	gezelter	1541
136	gezelter	1575	// work arrays for assembling potential energy
137			vector<potVec> pot_row;
138			vector<potVec> pot_col;
139	gezelter	1569
140	gezelter	1547	vector<int> identsRow;
141			vector<int> identsCol;
142	gezelter	1544
143	gezelter	1571	vector<AtomType*> atypesRow;
144			vector<AtomType*> atypesCol;
145
146	gezelter	1544	vector<int> AtomRowToGlobal;
147			vector<int> AtomColToGlobal;
148	gezelter	1569
149	gezelter	1544	vector<int> cgRowToGlobal;
150			vector<int> cgColToGlobal;
151	gezelter	1567
152	gezelter	1576	vector<RealType> groupCutoffRow;
153			vector<RealType> groupCutoffCol;
154			vector<int> groupColToGtype;
155			vector<int> groupRowToGtype;
156
157	gezelter	1568	vector<vector<int> > cellListRow_;
158			vector<vector<int> > cellListCol_;
159	gezelter	1569
160			vector<vector<int> > groupListRow_;
161			vector<vector<int> > groupListCol_;
162
163			vector<RealType> massFactorsRow;
164			vector<RealType> massFactorsCol;
165	gezelter	1539	#endif
166	gezelter	1567
167	gezelter	1539	};
168	chuckv	1538
169	gezelter	1539	}
170	chuckv	1538	#endif
171