src/parallel/ForceDecomposition.hpp

/*
 * Copyright (c) 2011 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_FORCEDECOMPOSITION_HPP
#define PARALLEL_FORCEDECOMPOSITION_HPP

#include "brains/SimInfo.hpp"
#include "brains/SnapshotManager.hpp"
#include "nonbonded/NonBondedInteraction.hpp"

using namespace std;
namespace OpenMD {
  
  /**
   * @class ForceDecomposition 
   *
   * ForceDecomposition is an interface for passing out and collecting
   * information from many processors at various stages of the main
   * non-bonded ForceLoop.
   *
   * The pairwise force calculation has an outer-running loop (the "I"
   * loop) and an inner-running loop (the "J" loop).  In parallel
   * decompositions, these loop over different groups of atoms on
   * different processors.  Between each set of computations on the
   * local processor, data must be exchanged among the processors.
   * This can happen at different times in the calculation:
   *
   *  distributeInitialData      (parallel communication - one time only)
   *  distributeData             (parallel communication - every ForceLoop)
   *
   *  loop iLoop over nLoops     (nLoops may be 1, 2, or until self consistent)
   *  |  loop over i
   *  |  | loop over j
   *  |  | | localComputation
   *  |  |  end
   *  |  end
   *  |  if (nLoops > 1):
   *  |  |   collectIntermediateData    (parallel communication)
   *  |  |   distributeIntermediateData (parallel communication)
   *  |  endif
   *  end
   * collectData                        (parallel communication)
   *
   * ForceDecomposition provides the interface for ForceLoop to do the
   * communication steps and to iterate using the correct set of atoms
   * and cutoff groups.
   */
  class ForceDecomposition {
  public:

    ForceDecomposition(SimInfo* info);
    virtual ~ForceDecomposition() {}
    
    virtual void distributeInitialData() = 0;
    virtual void distributeData() = 0;
    virtual void collectIntermediateData() = 0;
    virtual void distributeIntermediateData() = 0;
    virtual void collectData() = 0;

    // neighbor list routines
    virtual bool checkNeighborList();
    virtual vector<pair<int, int> >  buildNeighborList() = 0;

    // group bookkeeping
    virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;

    // Group->atom bookkeeping
    virtual vector<int> getAtomsInGroupRow(int cg1) = 0; 
    virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;

    virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
    virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
    virtual RealType getMassFactorRow(int atom1) = 0;
    virtual RealType getMassFactorColumn(int atom2) = 0;

    // spatial data
    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
       
    // atom bookkeeping
    virtual int getNAtomsInRow() = 0;
    virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
    virtual bool skipAtomPair(int atom1, int atom2) = 0;
    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;

    // filling interaction blocks with pointers
    virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
    virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
    virtual SelfData fillSelfData(int atom1);
    
  protected:
    SimInfo* info_;   
    SnapshotManager* sman_;    
    Snapshot* snap_;
    int storageLayout_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    

    map<pair<int, int>, int> topoDist; //< topoDist gives the
                                       //topological distance between
                                       //two atomic sites.  This
                                       //declaration is agnostic
                                       //regarding the parallel
                                       //decomposition.  The two
                                       //indices could be local or row
                                       //& column.  It will be up to
                                       //the specific decomposition
                                       //method to fill this.
    map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
                                       //to leave out of non-bonded
                                       //force evaluations.  This
                                       //declaration is agnostic
                                       //regarding the parallel
                                       //decomposition.  The two
                                       //indices could be local or row
                                       //& column.  It will be up to
                                       //the specific decomposition
                                       //method to fill this.

    vector<vector<int> > groupList_;
    vector<Vector3i> cellOffsets_;
    Vector3i nCells_;
    vector<vector<int> > cellList_;
    vector<Vector3d> saved_CG_positions_;

  };    
}
#endif
Revision:	1570
Committed:	Thu May 26 21:56:04 2011 UTC (13 years, 11 months ago) by gezelter
File size:	7130 byte(s)
Log Message:	More fixes
#	User	Rev	Content
1	gezelter	1539	/*
2	gezelter	1549	* Copyright (c) 2011 The University of Notre Dame. All Rights Reserved.
3	gezelter	1539	*
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
42	gezelter	1549	#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
43			#define PARALLEL_FORCEDECOMPOSITION_HPP
44	gezelter	1539
45	gezelter	1544	#include "brains/SimInfo.hpp"
46	gezelter	1568	#include "brains/SnapshotManager.hpp"
47	gezelter	1545	#include "nonbonded/NonBondedInteraction.hpp"
48	gezelter	1539
49			using namespace std;
50			namespace OpenMD {
51
52			/**
53	gezelter	1549	* @class ForceDecomposition
54	gezelter	1539	*
55	gezelter	1549	* ForceDecomposition is an interface for passing out and collecting
56			* information from many processors at various stages of the main
57			* non-bonded ForceLoop.
58			*
59	gezelter	1539	* The pairwise force calculation has an outer-running loop (the "I"
60			* loop) and an inner-running loop (the "J" loop). In parallel
61			* decompositions, these loop over different groups of atoms on
62			* different processors. Between each set of computations on the
63			* local processor, data must be exchanged among the processors.
64			* This can happen at different times in the calculation:
65			*
66			* distributeInitialData (parallel communication - one time only)
67			* distributeData (parallel communication - every ForceLoop)
68	gezelter	1544	*
69			* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
70			* \| loop over i
71			* \| \| loop over j
72			* \| \| \| localComputation
73			* \| \| end
74	gezelter	1539	* \| end
75	gezelter	1544	* \| if (nLoops > 1):
76			* \| \| collectIntermediateData (parallel communication)
77			* \| \| distributeIntermediateData (parallel communication)
78			* \| endif
79	gezelter	1539	* end
80	gezelter	1544	* collectData (parallel communication)
81	gezelter	1539	*
82	gezelter	1549	* ForceDecomposition provides the interface for ForceLoop to do the
83	gezelter	1539	* communication steps and to iterate using the correct set of atoms
84			* and cutoff groups.
85			*/
86	gezelter	1549	class ForceDecomposition {
87	gezelter	1539	public:
88
89	gezelter	1562	ForceDecomposition(SimInfo* info);
90	gezelter	1549	virtual ~ForceDecomposition() {}
91	gezelter	1539
92			virtual void distributeInitialData() = 0;
93			virtual void distributeData() = 0;
94			virtual void collectIntermediateData() = 0;
95			virtual void distributeIntermediateData() = 0;
96			virtual void collectData() = 0;
97
98	gezelter	1545	// neighbor list routines
99	gezelter	1568	virtual bool checkNeighborList();
100	gezelter	1545	virtual vector<pair<int, int> > buildNeighborList() = 0;
101	gezelter	1539
102	gezelter	1545	// group bookkeeping
103			virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
104	gezelter	1539
105	gezelter	1545	// Group->atom bookkeeping
106	gezelter	1569	virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
107	gezelter	1549	virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
108	gezelter	1569
109	gezelter	1549	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
110			virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
111	gezelter	1569	virtual RealType getMassFactorRow(int atom1) = 0;
112			virtual RealType getMassFactorColumn(int atom2) = 0;
113	gezelter	1545
114			// spatial data
115			virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
116			virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
117
118			// atom bookkeeping
119	gezelter	1570	virtual int getNAtomsInRow() = 0;
120			virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
121	gezelter	1545	virtual bool skipAtomPair(int atom1, int atom2) = 0;
122	gezelter	1549	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
123			virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
124	gezelter	1545
125			// filling interaction blocks with pointers
126			virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
127			virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
128	gezelter	1568	virtual SelfData fillSelfData(int atom1);
129	gezelter	1539
130			protected:
131	gezelter	1544	SimInfo* info_;
132	gezelter	1568	SnapshotManager* sman_;
133			Snapshot* snap_;
134			int storageLayout_;
135			RealType skinThickness_; /*< Verlet neighbor list skin thickness /
136
137	gezelter	1544	map<pair<int, int>, int> topoDist; //< topoDist gives the
138			//topological distance between
139			//two atomic sites. This
140			//declaration is agnostic
141			//regarding the parallel
142			//decomposition. The two
143			//indices could be local or row
144			//& column. It will be up to
145			//the specific decomposition
146			//method to fill this.
147			map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
148			//to leave out of non-bonded
149			//force evaluations. This
150			//declaration is agnostic
151			//regarding the parallel
152			//decomposition. The two
153			//indices could be local or row
154			//& column. It will be up to
155			//the specific decomposition
156			//method to fill this.
157	gezelter	1569
158			vector<vector<int> > groupList_;
159	gezelter	1562	vector<Vector3i> cellOffsets_;
160	gezelter	1568	Vector3i nCells_;
161			vector<vector<int> > cellList_;
162			vector<Vector3d> saved_CG_positions_;
163
164	gezelter	1539	};
165			}
166			#endif