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)
   * 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; }

    // 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;
    potVec excludedPot;

    /** 
     * 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:	1760
Committed:	Thu Jun 21 19:26:46 2012 UTC (13 years, 4 months ago) by gezelter
File size:	8025 byte(s)
Log Message:	Some bugfixes (CholeskyDecomposition), more work on fluctuating charges, migrating stats stuff into frameData
#	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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1539	*/
42
43	gezelter	1549	#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
44			#define PARALLEL_FORCEDECOMPOSITION_HPP
45	gezelter	1539
46	gezelter	1544	#include "brains/SimInfo.hpp"
47	gezelter	1568	#include "brains/SnapshotManager.hpp"
48	gezelter	1545	#include "nonbonded/NonBondedInteraction.hpp"
49	gezelter	1576	#include "nonbonded/Cutoffs.hpp"
50			#include "nonbonded/InteractionManager.hpp"
51			#include "utils/Tuple.hpp"
52	gezelter	1539
53			using namespace std;
54			namespace OpenMD {
55
56	gezelter	1576	typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57
58	gezelter	1539	/**
59	gezelter	1549	* @class ForceDecomposition
60	gezelter	1539	*
61	gezelter	1549	* 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	gezelter	1539	* 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	gezelter	1544	*
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	gezelter	1539	* \| end
81	gezelter	1544	* \| if (nLoops > 1):
82			* \| \| collectIntermediateData (parallel communication)
83			* \| \| distributeIntermediateData (parallel communication)
84			* \| endif
85	gezelter	1539	* end
86	gezelter	1544	* collectData (parallel communication)
87	gezelter	1760	* loop over i
88			* \| localComputation
89			* end
90			* collectSelfData (parallel communication)
91	gezelter	1539	*
92	gezelter	1549	* ForceDecomposition provides the interface for ForceLoop to do the
93	gezelter	1539	* communication steps and to iterate using the correct set of atoms
94			* and cutoff groups.
95			*/
96	gezelter	1549	class ForceDecomposition {
97	gezelter	1539	public:
98
99	gezelter	1579	ForceDecomposition(SimInfo* info, InteractionManager* iMan);
100	gezelter	1549	virtual ~ForceDecomposition() {}
101	gezelter	1539
102			virtual void distributeInitialData() = 0;
103			virtual void distributeData() = 0;
104	gezelter	1575	virtual void zeroWorkArrays() = 0;
105	gezelter	1539	virtual void collectIntermediateData() = 0;
106			virtual void distributeIntermediateData() = 0;
107			virtual void collectData() = 0;
108	gezelter	1756	virtual void collectSelfData() = 0;
109	gezelter	1583	virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
110			virtual potVec* getPairwisePotential() { return &pairwisePot; }
111	gezelter	1760	virtual potVec* getExcludedPotential() { return &excludedPot; }
112	gezelter	1539
113	gezelter	1545	// neighbor list routines
114	gezelter	1568	virtual bool checkNeighborList();
115	gezelter	1545	virtual vector<pair<int, int> > buildNeighborList() = 0;
116	gezelter	1539
117	gezelter	1576	// how to handle cutoffs:
118			void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
119			void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
120
121	gezelter	1545	// group bookkeeping
122	gezelter	1576	virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
123	gezelter	1723	virtual Vector3d getGroupVelocityColumn(int atom2) = 0;
124	gezelter	1539
125	gezelter	1545	// Group->atom bookkeeping
126	gezelter	1569	virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
127	gezelter	1549	virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
128	gezelter	1569
129	gezelter	1549	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
130			virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
131	gezelter	1569	virtual RealType getMassFactorRow(int atom1) = 0;
132			virtual RealType getMassFactorColumn(int atom2) = 0;
133	gezelter	1545
134			// spatial data
135			virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
136			virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
137
138			// atom bookkeeping
139	gezelter	1570	virtual int getNAtomsInRow() = 0;
140	gezelter	1587	virtual vector<int> getExcludesForAtom(int atom1) = 0;
141	gezelter	1756	virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
142	gezelter	1587	virtual bool excludeAtomPair(int atom1, int atom2) = 0;
143			virtual int getTopologicalDistance(int atom1, int atom2) = 0;
144	gezelter	1549	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
145			virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
146	gezelter	1723	virtual Vector3d getAtomVelocityColumn(int atom2) = 0;
147	gezelter	1545
148			// filling interaction blocks with pointers
149	gezelter	1582	virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
150			virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151	gezelter	1583
152	gezelter	1582	virtual void fillSelfData(SelfData &sdat, int atom1);
153	gezelter	1723
154			virtual void addToHeatFlux(Vector3d hf);
155			virtual void setHeatFlux(Vector3d hf);
156	gezelter	1539
157			protected:
158	gezelter	1544	SimInfo* info_;
159	gezelter	1568	SnapshotManager* sman_;
160			Snapshot* snap_;
161	gezelter	1571	ForceField* ff_;
162	gezelter	1576	InteractionManager* interactionMan_;
163
164	gezelter	1568	int storageLayout_;
165	gezelter	1723	bool needVelocities_;
166	gezelter	1568	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
167	gezelter	1576	RealType largestRcut_;
168	gezelter	1568
169	gezelter	1583	vector<int> idents;
170			potVec pairwisePot;
171			potVec embeddingPot;
172	gezelter	1760	potVec excludedPot;
173	gezelter	1583
174	gezelter	1579	/**
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	gezelter	1581	vector<vector<int> > topoDist;
184	gezelter	1587	vector<vector<int> > excludesForAtom;
185	gezelter	1569	vector<vector<int> > groupList_;
186	gezelter	1581	vector<RealType> massFactors;
187	gezelter	1591	vector<AtomType*> atypesLocal;
188	gezelter	1576
189	gezelter	1562	vector<Vector3i> cellOffsets_;
190	gezelter	1568	Vector3i nCells_;
191			vector<vector<int> > cellList_;
192			vector<Vector3d> saved_CG_positions_;
193
194	gezelter	1576	bool userChoseCutoff_;
195			RealType userCutoff_;
196			CutoffPolicy cutoffPolicy_;
197
198			map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
199
200	gezelter	1539	};
201			}
202			#endif