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"

#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_;    
#ifdef IS_MPI    
    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;
#endif
    vector<RealType> pot_local;
  };

}
#endif

Revision:	1549
Committed:	Wed Apr 27 18:38:15 2011 UTC (14 years ago) by gezelter
File size:	4912 byte(s)
Log Message:	a few more tweaks We're getting somewhat closer to deleting fortran.
#	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	1549	#include "Parallel/ForceDecomposition.hpp"
46	gezelter	1539	#include "math/SquareMatrix3.hpp"
47	chuckv	1538
48	gezelter	1544	#ifdef IS_MPI
49			#include "Parallel/Communicator.hpp"
50			#endif
51
52	gezelter	1541	using namespace std;
53	gezelter	1539	namespace OpenMD {
54	chuckv	1538
55	gezelter	1549	class ForceMatrixDecomposition : public ForceDecomposition {
56	gezelter	1539	public:
57	gezelter	1549	ForceMatrixDecomposition(SimInfo* info) : ForceDecomposition(info) {sman_ = info_->getSnapshotManager();}
58	gezelter	1539	void distributeInitialData();
59			void distributeData();
60			void collectIntermediateData();
61			void distributeIntermediateData();
62			void collectData();
63	chuckv	1538
64	gezelter	1549	// neighbor list routines
65			bool checkNeighborList();
66			vector<pair<int, int> > buildNeighborList();
67	chuckv	1538
68	gezelter	1549	// group bookkeeping
69			pair<int, int> getGroupTypes(int cg1, int cg2);
70	chuckv	1538
71	gezelter	1549	// Group->atom bookkeeping
72			vector<int> getAtomsInGroupRow(int cg1);
73			vector<int> getAtomsInGroupColumn(int cg2);
74			Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
75			Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
76			RealType getMfactRow(int atom1);
77			RealType getMfactColumn(int atom2);
78	chuckv	1538
79	gezelter	1549	// spatial data
80			Vector3d getIntergroupVector(int cg1, int cg2);
81			Vector3d getInteratomicVector(int atom1, int atom2);
82
83			// atom bookkeeping
84			vector<int> getAtomList();
85			vector<int> getSkipsForAtom(int atom1);
86			bool skipAtomPair(int atom1, int atom2);
87			void addForceToAtomRow(int atom1, Vector3d fg);
88			void addForceToAtomColumn(int atom2, Vector3d fg);
89
90			// filling interaction blocks with pointers
91			InteractionData fillInteractionData(int atom1, int atom2);
92			InteractionData fillSkipData(int atom1, int atom2);
93			SelfData fillSelfData(int atom1);
94
95	gezelter	1544	private:
96			SnapshotManager* sman_;
97			#ifdef IS_MPI
98	gezelter	1549	Communicator<Row, int>* AtomCommIntRow;
99			Communicator<Row, RealType>* AtomCommRealRow;
100			Communicator<Row, Vector3d>* AtomCommVectorRow;
101			Communicator<Row, Mat3x3d>* AtomCommMatrixRow;
102	chuckv	1538
103	gezelter	1549	Communicator<Column, int>* AtomCommIntColumn;
104			Communicator<Column, RealType>* AtomCommRealColumn;
105			Communicator<Column, Vector3d>* AtomCommVectorColumn;
106			Communicator<Column, Mat3x3d>* AtomCommMatrixColumn;
107	chuckv	1538
108	gezelter	1549	Communicator<Row, int>* cgCommIntRow;
109			Communicator<Row, Vector3d>* cgCommVectorRow;
110			Communicator<Column, int>* cgCommIntColumn;
111			Communicator<Column, Vector3d>* cgCommVectorColumn;
112	gezelter	1541
113			vector<vector<RealType> > pot_row;
114			vector<vector<RealType> > pot_col;
115	gezelter	1547	vector<int> identsRow;
116			vector<int> identsCol;
117	gezelter	1544
118			vector<int> AtomLocalToGlobal;
119			vector<int> AtomRowToGlobal;
120			vector<int> AtomColToGlobal;
121			vector<int> cgLocalToGlobal;
122			vector<int> cgRowToGlobal;
123			vector<int> cgColToGlobal;
124	gezelter	1539	#endif
125	gezelter	1544	vector<RealType> pot_local;
126	gezelter	1539	};
127	chuckv	1538
128	gezelter	1539	}
129	chuckv	1538	#endif
130