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]  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 collectData();

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

    // group bookkeeping
    groupCutoffs getGroupCutoffs(int cg1, int cg2);
    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);
    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);
    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> 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;

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

private:
    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:	1723
Committed:	Thu May 24 20:59:54 2012 UTC (12 years, 11 months ago) by gezelter
File size:	5896 byte(s)
Log Message:	Bug fixes for heat flux import
#	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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
44	#define PARALLEL_FORCEMATRIXDECOMPOSITION_HPP
45
46	#include "parallel/ForceDecomposition.hpp"
47	#include "math/SquareMatrix3.hpp"
48	#include "brains/Snapshot.hpp"
49
50	#ifdef IS_MPI
51	#include "parallel/Communicator.hpp"
52	#endif
53
54	using namespace std;
55	namespace OpenMD {
56
57	class ForceMatrixDecomposition : public ForceDecomposition {
58	public:
59	ForceMatrixDecomposition(SimInfo* info, InteractionManager* iMan);
60
61	void distributeInitialData();
62	void zeroWorkArrays();
63	void distributeData();
64	void collectIntermediateData();
65	void distributeIntermediateData();
66	void collectData();
67
68	// neighbor list routines
69	vector<pair<int, int> > buildNeighborList();
70
71	// group bookkeeping
72	groupCutoffs getGroupCutoffs(int cg1, int cg2);
73	Vector3d getGroupVelocityColumn(int cg2);
74
75	// 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	RealType getMassFactorRow(int atom1);
81	RealType getMassFactorColumn(int atom2);
82
83	// spatial data
84	Vector3d getIntergroupVector(int cg1, int cg2);
85	Vector3d getInteratomicVector(int atom1, int atom2);
86
87	// atom bookkeeping
88	int getNAtomsInRow();
89	int getTopologicalDistance(int atom1, int atom2);
90	vector<int> getExcludesForAtom(int atom1);
91	bool skipAtomPair(int atom1, int atom2);
92	bool excludeAtomPair(int atom1, int atom2);
93	void addForceToAtomRow(int atom1, Vector3d fg);
94	void addForceToAtomColumn(int atom2, Vector3d fg);
95	Vector3d getAtomVelocityColumn(int atom2);
96
97	// filling interaction blocks with pointers
98	void fillInteractionData(InteractionData &idat, int atom1, int atom2);
99	void unpackInteractionData(InteractionData &idat, int atom1, int atom2);
100
101	private:
102	void createGtypeCutoffMap();
103
104	int nLocal_;
105	int nGroups_;
106	vector<int> AtomLocalToGlobal;
107	vector<int> cgLocalToGlobal;
108	vector<RealType> groupCutoff;
109	vector<int> groupToGtype;
110
111	#ifdef IS_MPI
112	DataStorage atomRowData; DataStorage atomColData;
113	DataStorage cgRowData;
114	DataStorage cgColData;
115
116	int nAtomsInRow_;
117	int nAtomsInCol_;
118	int nGroupsInRow_;
119	int nGroupsInCol_;
120
121	Communicator<Row> rowComm;
122	Communicator<Column> colComm;
123
124	Plan<int>* AtomPlanIntRow;
125	Plan<RealType>* AtomPlanRealRow;
126	Plan<Vector3d>* AtomPlanVectorRow;
127	Plan<Mat3x3d>* AtomPlanMatrixRow;
128	Plan<potVec>* AtomPlanPotRow;
129
130	Plan<int>* AtomPlanIntColumn;
131	Plan<RealType>* AtomPlanRealColumn;
132	Plan<Vector3d>* AtomPlanVectorColumn;
133	Plan<Mat3x3d>* AtomPlanMatrixColumn;
134	Plan<potVec>* AtomPlanPotColumn;
135
136	Plan<int>* cgPlanIntRow;
137	Plan<Vector3d>* cgPlanVectorRow;
138	Plan<int>* cgPlanIntColumn;
139	Plan<Vector3d>* cgPlanVectorColumn;
140
141	// work arrays for assembling potential energy
142	vector<potVec> pot_row;
143	vector<potVec> pot_col;
144
145	vector<int> identsRow;
146	vector<int> identsCol;
147
148	vector<AtomType*> atypesRow;
149	vector<AtomType*> atypesCol;
150
151	vector<int> AtomRowToGlobal;
152	vector<int> AtomColToGlobal;
153
154	public:
155	vector<int> cgRowToGlobal;
156	vector<int> cgColToGlobal;
157
158	private:
159	vector<RealType> groupCutoffRow;
160	vector<RealType> groupCutoffCol;
161	vector<int> groupColToGtype;
162	vector<int> groupRowToGtype;
163
164	vector<vector<int> > cellListRow_;
165	vector<vector<int> > cellListCol_;
166
167	vector<vector<int> > groupListRow_;
168	vector<vector<int> > groupListCol_;
169
170	vector<RealType> massFactorsRow;
171	vector<RealType> massFactorsCol;
172	#endif
173
174	};
175
176	}
177	#endif
178