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);

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

    // neighbor list routines
    vector<pair<int, int> >  buildNeighborList();
    // neighbor list routines based on Rapaport
    vector<vector<CutoffGroup *> > buildLayerBasedNeighborList();

    // 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 getIntergroupVector(CutoffGroup *cg1, CutoffGroup *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);

    // memory reordering
    void reorderGroupCutoffs(vector<int> &order);
    void reorderPosition(vector<int> &order);
    void reorderGroupList(vector<int> &order);
    void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);

  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> 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<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:	1598
Committed:	Wed Jul 27 14:26:53 2011 UTC (13 years, 9 months ago) by mciznick
File size:	6137 byte(s)
Log Message:	Updated ordered neighbor list generation.
#	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	1593	ForceMatrixDecomposition(SimInfo* info, InteractionManager* 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	1595	// neighbor list routines based on Rapaport
70	mciznick	1598	vector<vector<CutoffGroup *> > buildLayerBasedNeighborList();
71	chuckv	1538
72	gezelter	1549	// group bookkeeping
73	gezelter	1576	groupCutoffs getGroupCutoffs(int cg1, int cg2);
74	chuckv	1538
75	gezelter	1549	// Group->atom bookkeeping
76			vector<int> getAtomsInGroupRow(int cg1);
77			vector<int> getAtomsInGroupColumn(int cg2);
78			Vector3d getAtomToGroupVectorRow(int atom1, int cg1);
79			Vector3d getAtomToGroupVectorColumn(int atom2, int cg2);
80	gezelter	1569	RealType getMassFactorRow(int atom1);
81			RealType getMassFactorColumn(int atom2);
82	chuckv	1538
83	gezelter	1549	// spatial data
84			Vector3d getIntergroupVector(int cg1, int cg2);
85	mciznick	1598	Vector3d getIntergroupVector(CutoffGroup cg1, CutoffGroup cg2);
86	gezelter	1549	Vector3d getInteratomicVector(int atom1, int atom2);
87
88			// atom bookkeeping
89	gezelter	1570	int getNAtomsInRow();
90	gezelter	1579	int getTopologicalDistance(int atom1, int atom2);
91	gezelter	1587	vector<int> getExcludesForAtom(int atom1);
92	gezelter	1549	bool skipAtomPair(int atom1, int atom2);
93	gezelter	1587	bool excludeAtomPair(int atom1, int atom2);
94	gezelter	1549	void addForceToAtomRow(int atom1, Vector3d fg);
95			void addForceToAtomColumn(int atom2, Vector3d fg);
96
97			// filling interaction blocks with pointers
98	gezelter	1582	void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99			void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100	gezelter	1549
101	mciznick	1598	// memory reordering
102			void reorderGroupCutoffs(vector<int> &order);
103			void reorderPosition(vector<int> &order);
104			void reorderGroupList(vector<int> &order);
105			void reorderMemory(vector<vector<CutoffGroup *> > &H_c_l);
106
107	gezelter	1544	private:
108	gezelter	1576	void createGtypeCutoffMap();
109
110	gezelter	1567	int nLocal_;
111			int nGroups_;
112	gezelter	1569	vector<int> AtomLocalToGlobal;
113			vector<int> cgLocalToGlobal;
114	gezelter	1576	vector<RealType> groupCutoff;
115			vector<int> groupToGtype;
116	gezelter	1567
117	gezelter	1544	#ifdef IS_MPI
118	gezelter	1551	DataStorage atomRowData;
119			DataStorage atomColData;
120			DataStorage cgRowData;
121			DataStorage cgColData;
122
123	gezelter	1567	int nAtomsInRow_;
124			int nAtomsInCol_;
125			int nGroupsInRow_;
126			int nGroupsInCol_;
127
128	gezelter	1593	Communicator<Row> rowComm;
129			Communicator<Column> colComm;
130	chuckv	1538
131	gezelter	1593	Plan<int>* AtomPlanIntRow;
132			Plan<RealType>* AtomPlanRealRow;
133			Plan<Vector3d>* AtomPlanVectorRow;
134			Plan<Mat3x3d>* AtomPlanMatrixRow;
135			Plan<potVec>* AtomPlanPotRow;
136	chuckv	1538
137	gezelter	1593	Plan<int>* AtomPlanIntColumn;
138			Plan<RealType>* AtomPlanRealColumn;
139			Plan<Vector3d>* AtomPlanVectorColumn;
140			Plan<Mat3x3d>* AtomPlanMatrixColumn;
141			Plan<potVec>* AtomPlanPotColumn;
142	gezelter	1541
143	gezelter	1593	Plan<int>* cgPlanIntRow;
144			Plan<Vector3d>* cgPlanVectorRow;
145			Plan<int>* cgPlanIntColumn;
146			Plan<Vector3d>* cgPlanVectorColumn;
147
148	gezelter	1575	// work arrays for assembling potential energy
149			vector<potVec> pot_row;
150			vector<potVec> pot_col;
151	gezelter	1569
152	gezelter	1547	vector<int> identsRow;
153			vector<int> identsCol;
154	gezelter	1544
155	gezelter	1571	vector<AtomType*> atypesRow;
156			vector<AtomType*> atypesCol;
157
158	gezelter	1544	vector<int> AtomRowToGlobal;
159			vector<int> AtomColToGlobal;
160	gezelter	1569
161	gezelter	1544	vector<int> cgRowToGlobal;
162			vector<int> cgColToGlobal;
163	gezelter	1567
164	gezelter	1576	vector<RealType> groupCutoffRow;
165			vector<RealType> groupCutoffCol;
166			vector<int> groupColToGtype;
167			vector<int> groupRowToGtype;
168
169	gezelter	1568	vector<vector<int> > cellListRow_;
170			vector<vector<int> > cellListCol_;
171	gezelter	1569
172			vector<vector<int> > groupListRow_;
173			vector<vector<int> > groupListCol_;
174
175			vector<RealType> massFactorsRow;
176			vector<RealType> massFactorsCol;
177	gezelter	1539	#endif
178	gezelter	1567
179	gezelter	1539	};
180	chuckv	1538
181	gezelter	1539	}
182	chuckv	1538	#endif
183