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

#include "brains/SimInfo.hpp"
#include "brains/SnapshotManager.hpp"
#include "nonbonded/NonBondedInteraction.hpp"
#include "nonbonded/InteractionManager.hpp"
#include "utils/Tuple.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)
   * loop over i
   * | localComputation
   * end
   * collectSelfData                    (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, InteractionManager* iMan);
    virtual ~ForceDecomposition() {}
    
    virtual void distributeInitialData() = 0;
    virtual void distributeData() = 0;
    virtual void zeroWorkArrays() = 0;
    virtual void collectIntermediateData() = 0;
    virtual void distributeIntermediateData() = 0;
    virtual void collectData() = 0;
    virtual void collectSelfData() = 0;
    virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
    virtual potVec* getPairwisePotential() { return &pairwisePot; }
    virtual potVec* getExcludedPotential() { return &excludedPot; }
    virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }

    // neighbor list routines
    virtual bool checkNeighborList();
    virtual void buildNeighborList(vector<int>& neighborList, vector<int>& point) = 0;

    void setCutoffRadius(RealType rCut);
    
    // group bookkeeping
    virtual Vector3d& getGroupVelocityColumn(int atom2) = 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>& getExcludesForAtom(int atom1) = 0;
    virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
    virtual bool excludeAtomPair(int atom1, int atom2) = 0;
    virtual int getTopologicalDistance(int atom1, int atom2) = 0;
    virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
    virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
    virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;

    // filling interaction blocks with pointers
    virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true) = 0;
    virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;

    virtual void fillSelfData(SelfData &sdat, int atom1);

    virtual void addToHeatFlux(Vector3d hf);
    virtual void setHeatFlux(Vector3d hf);
    
  protected:
    SimInfo* info_;   
    SnapshotManager* sman_;    
    Snapshot* snap_;
    ForceField* ff_;
    InteractionManager* interactionMan_;

    int storageLayout_;
    bool needVelocities_;
    bool usePeriodicBoundaryConditions_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */
    RealType rCut_;
    RealType rList_;
    RealType rListSq_;

    vector<int> idents;
    vector<int> regions;
    potVec pairwisePot;
    potVec embeddingPot;
    potVec excludedPot;
    potVec excludedSelfPot;

    /** 
     * The topological distance between two atomic sites is handled
     * via two vector structures for speed.  These structures agnostic
     * regarding the parallel decomposition.  The index for
     * toposForAtom could be local or row, while the values could be
     * local or column.  It will be up to the specific decomposition
     * method to fill these.
     */
    vector<vector<int> > toposForAtom; 
    vector<vector<int> > topoDist;                                       
    vector<vector<int> > excludesForAtom;
    vector<vector<int> > groupList_;
    vector<RealType> massFactors;
    vector<AtomType*> atypesLocal;

    vector<Vector3i> cellOffsets_;
    Vector3i nCells_;
    vector<vector<int> > cellList_;
    vector<Vector3d> saved_CG_positions_;
  };    
}
#endif
Revision:	2057
Committed:	Tue Mar 3 15:22:26 2015 UTC (10 years, 1 month ago) by gezelter
File size:	7822 byte(s)
Log Message:	Performance improvements, Removed CutoffPolicy
#	Content
1	/*
2	* Copyright (c) 2011 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, 234107 (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_FORCEDECOMPOSITION_HPP
44	#define PARALLEL_FORCEDECOMPOSITION_HPP
45
46	#include "brains/SimInfo.hpp"
47	#include "brains/SnapshotManager.hpp"
48	#include "nonbonded/NonBondedInteraction.hpp"
49	#include "nonbonded/InteractionManager.hpp"
50	#include "utils/Tuple.hpp"
51
52	using namespace std;
53	namespace OpenMD {
54
55	/**
56	* @class ForceDecomposition
57	*
58	* ForceDecomposition is an interface for passing out and collecting
59	* information from many processors at various stages of the main
60	* non-bonded ForceLoop.
61	*
62	* The pairwise force calculation has an outer-running loop (the "I"
63	* loop) and an inner-running loop (the "J" loop). In parallel
64	* decompositions, these loop over different groups of atoms on
65	* different processors. Between each set of computations on the
66	* local processor, data must be exchanged among the processors.
67	* This can happen at different times in the calculation:
68	*
69	* distributeInitialData (parallel communication - one time only)
70	* distributeData (parallel communication - every ForceLoop)
71	*
72	* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
73	* \| loop over i
74	* \| \| loop over j
75	* \| \| \| localComputation
76	* \| \| end
77	* \| end
78	* \| if (nLoops > 1):
79	* \| \| collectIntermediateData (parallel communication)
80	* \| \| distributeIntermediateData (parallel communication)
81	* \| endif
82	* end
83	* collectData (parallel communication)
84	* loop over i
85	* \| localComputation
86	* end
87	* collectSelfData (parallel communication)
88	*
89	* ForceDecomposition provides the interface for ForceLoop to do the
90	* communication steps and to iterate using the correct set of atoms
91	* and cutoff groups.
92	*/
93	class ForceDecomposition {
94	public:
95
96	ForceDecomposition(SimInfo* info, InteractionManager* iMan);
97	virtual ~ForceDecomposition() {}
98
99	virtual void distributeInitialData() = 0;
100	virtual void distributeData() = 0;
101	virtual void zeroWorkArrays() = 0;
102	virtual void collectIntermediateData() = 0;
103	virtual void distributeIntermediateData() = 0;
104	virtual void collectData() = 0;
105	virtual void collectSelfData() = 0;
106	virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
107	virtual potVec* getPairwisePotential() { return &pairwisePot; }
108	virtual potVec* getExcludedPotential() { return &excludedPot; }
109	virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }
110
111	// neighbor list routines
112	virtual bool checkNeighborList();
113	virtual void buildNeighborList(vector<int>& neighborList, vector<int>& point) = 0;
114
115	void setCutoffRadius(RealType rCut);
116
117	// group bookkeeping
118	virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
119
120	// Group->atom bookkeeping
121	virtual vector<int>& getAtomsInGroupRow(int cg1) = 0;
122	virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0;
123
124	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
125	virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
126	virtual RealType& getMassFactorRow(int atom1) = 0;
127	virtual RealType& getMassFactorColumn(int atom2) = 0;
128
129	// spatial data
130	virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
131	virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
132
133	// atom bookkeeping
134	virtual int& getNAtomsInRow() = 0;
135	virtual vector<int>& getExcludesForAtom(int atom1) = 0;
136	virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
137	virtual bool excludeAtomPair(int atom1, int atom2) = 0;
138	virtual int getTopologicalDistance(int atom1, int atom2) = 0;
139	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
140	virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
141	virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;
142
143	// filling interaction blocks with pointers
144	virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2, bool newAtom1 = true) = 0;
145	virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
146
147	virtual void fillSelfData(SelfData &sdat, int atom1);
148
149	virtual void addToHeatFlux(Vector3d hf);
150	virtual void setHeatFlux(Vector3d hf);
151
152	protected:
153	SimInfo* info_;
154	SnapshotManager* sman_;
155	Snapshot* snap_;
156	ForceField* ff_;
157	InteractionManager* interactionMan_;
158
159	int storageLayout_;
160	bool needVelocities_;
161	bool usePeriodicBoundaryConditions_;
162	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
163	RealType rCut_;
164	RealType rList_;
165	RealType rListSq_;
166
167	vector<int> idents;
168	vector<int> regions;
169	potVec pairwisePot;
170	potVec embeddingPot;
171	potVec excludedPot;
172	potVec excludedSelfPot;
173
174	/**
175	* The topological distance between two atomic sites is handled
176	* via two vector structures for speed. These structures agnostic
177	* regarding the parallel decomposition. The index for
178	* toposForAtom could be local or row, while the values could be
179	* local or column. It will be up to the specific decomposition
180	* method to fill these.
181	*/
182	vector<vector<int> > toposForAtom;
183	vector<vector<int> > topoDist;
184	vector<vector<int> > excludesForAtom;
185	vector<vector<int> > groupList_;
186	vector<RealType> massFactors;
187	vector<AtomType*> atypesLocal;
188
189	vector<Vector3i> cellOffsets_;
190	Vector3i nCells_;
191	vector<vector<int> > cellList_;
192	vector<Vector3d> saved_CG_positions_;
193	};
194	}
195	#endif