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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#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);

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

    // neighbor list routines
    void buildNeighborList(vector<int>& neighborList, vector<int>& point);

    // group bookkeeping
    Vector3d& getGroupVelocityColumn(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, int cg1, int cg2);
    bool excludeAtomPair(int atom1, int atom2);
    void addForceToAtomRow(int atom1, Vector3d fg);
    void addForceToAtomColumn(int atom2, Vector3d fg);
    Vector3d& getAtomVelocityColumn(int atom2);

    // filling interaction blocks with pointers
    void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true);
    void unpackInteractionData(InteractionData &idat, int atom1, int atom2);

  private:     
    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> rowComm;
    Communicator<Column> colComm;

    Plan<int>* AtomPlanIntRow;
    Plan<RealType>* AtomPlanRealRow; 
    Plan<Vector3d>* AtomPlanVectorRow; 
    Plan<Mat3x3d>*  AtomPlanMatrixRow; 
    Plan<potVec>* AtomPlanPotRow;

    Plan<int>* AtomPlanIntColumn;
    Plan<RealType>* AtomPlanRealColumn; 
    Plan<Vector3d>* AtomPlanVectorColumn; 
    Plan<Mat3x3d>*  AtomPlanMatrixColumn;
    Plan<potVec>* AtomPlanPotColumn; 

    Plan<int>* cgPlanIntRow;
    Plan<Vector3d>* cgPlanVectorRow; 
    Plan<int>* cgPlanIntColumn;
    Plan<Vector3d>* cgPlanVectorColumn; 

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

    vector<potVec> expot_row;
    vector<potVec> expot_col;

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

    vector<int> regionsRow;
    vector<int> regionsCol;

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

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

public:
    vector<int> cgRowToGlobal;
    vector<int> cgColToGlobal;

private:
    vector<vector<int> > cellListRow_;
    vector<vector<int> > cellListCol_;

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

    vector<RealType> massFactorsRow;
    vector<RealType> massFactorsCol;

    vector<int> regionRow;
    vector<int> regionCol;
#endif

  };

}
#endif

Revision:	2064
Committed:	Tue Mar 3 17:02:20 2015 UTC (10 years, 8 months ago) by gezelter
File size:	5949 byte(s)
Log Message:	Removed inlining, updated papers & copyright
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	chuckv	1538	*/
42	gezelter	1539
43	gezelter	1549	#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44			#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
45	chuckv	1538
46	gezelter	1567	#include "parallel/ForceDecomposition.hpp"
47	gezelter	1539	#include "math/SquareMatrix3.hpp"
48	gezelter	1551	#include "brains/Snapshot.hpp"
49	chuckv	1538
50	gezelter	1544	#ifdef IS_MPI
51	gezelter	1567	#include "parallel/Communicator.hpp"
52	gezelter	1544	#endif
53
54	gezelter	1541	using namespace std;
55	gezelter	1539	namespace OpenMD {
56	chuckv	1538
57	gezelter	1549	class ForceMatrixDecomposition : public ForceDecomposition {
58	gezelter	1539	public:
59	gezelter	1593	ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60	gezelter	1568
61	gezelter	1539	void distributeInitialData();
62	gezelter	1575	void zeroWorkArrays();
63	gezelter	1539	void distributeData();
64			void collectIntermediateData();
65			void distributeIntermediateData();
66	gezelter	1756	void collectSelfData();
67	gezelter	1539	void collectData();
68	chuckv	1538
69	gezelter	1549	// neighbor list routines
70	gezelter	2057	void buildNeighborList(vector<int>& neighborList, vector<int>& point);
71	chuckv	1538
72	gezelter	1549	// group bookkeeping
73	gezelter	1893	Vector3d& getGroupVelocityColumn(int cg2);
74	chuckv	1538
75	gezelter	1549	// Group->atom bookkeeping
76	gezelter	1893	vector<int>& getAtomsInGroupRow(int cg1);
77			vector<int>& getAtomsInGroupColumn(int cg2);
78	gezelter	1549	Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
79			Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
80	gezelter	1893	RealType& getMassFactorRow(int atom1);
81			RealType& getMassFactorColumn(int atom2);
82	chuckv	1538
83	gezelter	1549	// spatial data
84	gezelter	2064	Vector3d getIntergroupVector(int cg1, int cg2);
85			Vector3d getInteratomicVector(int atom1, int atom2);
86	gezelter	1549
87			// atom bookkeeping
88	gezelter	1893	int& getNAtomsInRow();
89	gezelter	1579	int getTopologicalDistance(int atom1, int atom2);
90	gezelter	1893	vector<int>& getExcludesForAtom(int atom1);
91	gezelter	1756	bool skipAtomPair(int atom1, int atom2, int cg1, int cg2);
92	gezelter	1587	bool excludeAtomPair(int atom1, int atom2);
93	gezelter	1549	void addForceToAtomRow(int atom1, Vector3d fg);
94			void addForceToAtomColumn(int atom2, Vector3d fg);
95	gezelter	1893	Vector3d& getAtomVelocityColumn(int atom2);
96	gezelter	1549
97			// filling interaction blocks with pointers
98	gezelter	2057	void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true);
99	gezelter	1582	void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100	gezelter	1549
101	gezelter	2057	private:
102	gezelter	1567	int nLocal_;
103			int nGroups_;
104	gezelter	1569	vector<int> AtomLocalToGlobal;
105			vector<int> cgLocalToGlobal;
106	gezelter	1576	vector<RealType> groupCutoff;
107			vector<int> groupToGtype;
108	gezelter	1567
109	gezelter	1544	#ifdef IS_MPI
110	gezelter	1930	DataStorage atomRowData;
111			DataStorage atomColData;
112	gezelter	1551	DataStorage cgRowData;
113			DataStorage cgColData;
114
115	gezelter	1567	int nAtomsInRow_;
116			int nAtomsInCol_;
117			int nGroupsInRow_;
118			int nGroupsInCol_;
119
120	gezelter	1593	Communicator<Row> rowComm;
121			Communicator<Column> colComm;
122	chuckv	1538
123	gezelter	1593	Plan<int>* AtomPlanIntRow;
124			Plan<RealType>* AtomPlanRealRow;
125			Plan<Vector3d>* AtomPlanVectorRow;
126			Plan<Mat3x3d>* AtomPlanMatrixRow;
127			Plan<potVec>* AtomPlanPotRow;
128	chuckv	1538
129	gezelter	1593	Plan<int>* AtomPlanIntColumn;
130			Plan<RealType>* AtomPlanRealColumn;
131			Plan<Vector3d>* AtomPlanVectorColumn;
132			Plan<Mat3x3d>* AtomPlanMatrixColumn;
133			Plan<potVec>* AtomPlanPotColumn;
134	gezelter	1541
135	gezelter	1593	Plan<int>* cgPlanIntRow;
136			Plan<Vector3d>* cgPlanVectorRow;
137			Plan<int>* cgPlanIntColumn;
138			Plan<Vector3d>* cgPlanVectorColumn;
139
140	gezelter	1575	// work arrays for assembling potential energy
141			vector<potVec> pot_row;
142			vector<potVec> pot_col;
143	gezelter	1569
144	gezelter	1760	vector<potVec> expot_row;
145			vector<potVec> expot_col;
146
147	gezelter	1547	vector<int> identsRow;
148			vector<int> identsCol;
149	gezelter	1544
150	gezelter	1929	vector<int> regionsRow;
151			vector<int> regionsCol;
152
153	gezelter	1571	vector<AtomType*> atypesRow;
154			vector<AtomType*> atypesCol;
155
156	gezelter	1544	vector<int> AtomRowToGlobal;
157			vector<int> AtomColToGlobal;
158	gezelter	1569
159	gezelter	1612	public:
160	gezelter	1544	vector<int> cgRowToGlobal;
161			vector<int> cgColToGlobal;
162	gezelter	1567
163	gezelter	1612	private:
164	gezelter	1568	vector<vector<int> > cellListRow_;
165			vector<vector<int> > cellListCol_;
166	gezelter	1569
167			vector<vector<int> > groupListRow_;
168			vector<vector<int> > groupListCol_;
169
170			vector<RealType> massFactorsRow;
171			vector<RealType> massFactorsCol;
172	gezelter	1930
173			vector<int> regionRow;
174			vector<int> regionCol;
175	gezelter	1539	#endif
176	gezelter	1567
177	gezelter	1539	};
178	chuckv	1538
179	gezelter	1539	}
180	chuckv	1538	#endif
181