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]  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/Cutoffs.hpp"
#include "nonbonded/InteractionManager.hpp"
#include "utils/Tuple.hpp"

using namespace std;
namespace OpenMD {
  
  typedef tuple3<RealType, RealType, RealType> groupCutoffs;

  /**
   * @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, 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; }

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

    // how to handle cutoffs:
    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }

    // group bookkeeping
    virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
    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) = 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_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
    RealType largestRcut_;

    vector<int> idents;
    potVec pairwisePot;
    potVec embeddingPot;

    /** 
     * 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_;

    bool userChoseCutoff_;
    RealType userCutoff_;
    CutoffPolicy cutoffPolicy_;

    map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;

  };    
}
#endif
Revision:	1756
Committed:	Mon Jun 18 18:23:20 2012 UTC (12 years, 10 months ago) by gezelter
File size:	7818 byte(s)
Log Message:	bugfixes for self interactions (particularly in parallel)
#	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, 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_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/Cutoffs.hpp"
50	#include "nonbonded/InteractionManager.hpp"
51	#include "utils/Tuple.hpp"
52
53	using namespace std;
54	namespace OpenMD {
55
56	typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57
58	/**
59	* @class ForceDecomposition
60	*
61	* ForceDecomposition is an interface for passing out and collecting
62	* information from many processors at various stages of the main
63	* non-bonded ForceLoop.
64	*
65	* The pairwise force calculation has an outer-running loop (the "I"
66	* loop) and an inner-running loop (the "J" loop). In parallel
67	* decompositions, these loop over different groups of atoms on
68	* different processors. Between each set of computations on the
69	* local processor, data must be exchanged among the processors.
70	* This can happen at different times in the calculation:
71	*
72	* distributeInitialData (parallel communication - one time only)
73	* distributeData (parallel communication - every ForceLoop)
74	*
75	* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
76	* \| loop over i
77	* \| \| loop over j
78	* \| \| \| localComputation
79	* \| \| end
80	* \| end
81	* \| if (nLoops > 1):
82	* \| \| collectIntermediateData (parallel communication)
83	* \| \| distributeIntermediateData (parallel communication)
84	* \| endif
85	* end
86	* collectData (parallel communication)
87	*
88	* ForceDecomposition provides the interface for ForceLoop to do the
89	* communication steps and to iterate using the correct set of atoms
90	* and cutoff groups.
91	*/
92	class ForceDecomposition {
93	public:
94
95	ForceDecomposition(SimInfo* info, InteractionManager* iMan);
96	virtual ~ForceDecomposition() {}
97
98	virtual void distributeInitialData() = 0;
99	virtual void distributeData() = 0;
100	virtual void zeroWorkArrays() = 0;
101	virtual void collectIntermediateData() = 0;
102	virtual void distributeIntermediateData() = 0;
103	virtual void collectData() = 0;
104	virtual void collectSelfData() = 0;
105	virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
106	virtual potVec* getPairwisePotential() { return &pairwisePot; }
107
108	// neighbor list routines
109	virtual bool checkNeighborList();
110	virtual vector<pair<int, int> > buildNeighborList() = 0;
111
112	// how to handle cutoffs:
113	void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
114	void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
115
116	// group bookkeeping
117	virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
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) = 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	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
162	RealType largestRcut_;
163
164	vector<int> idents;
165	potVec pairwisePot;
166	potVec embeddingPot;
167
168	/**
169	* The topological distance between two atomic sites is handled
170	* via two vector structures for speed. These structures agnostic
171	* regarding the parallel decomposition. The index for
172	* toposForAtom could be local or row, while the values could be
173	* local or column. It will be up to the specific decomposition
174	* method to fill these.
175	*/
176	vector<vector<int> > toposForAtom;
177	vector<vector<int> > topoDist;
178	vector<vector<int> > excludesForAtom;
179	vector<vector<int> > groupList_;
180	vector<RealType> massFactors;
181	vector<AtomType*> atypesLocal;
182
183	vector<Vector3i> cellOffsets_;
184	Vector3i nCells_;
185	vector<vector<int> > cellList_;
186	vector<Vector3d> saved_CG_positions_;
187
188	bool userChoseCutoff_;
189	RealType userCutoff_;
190	CutoffPolicy cutoffPolicy_;
191
192	map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
193
194	};
195	}
196	#endif