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"
#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);
    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 potVec getLongRangePotential() { return longRangePot_; }

    // 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;

    // 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 void unpackInteractionData(InteractionData idat, 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_;
    ForceField* ff_;
    InteractionManager* interactionMan_;

    int storageLayout_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
    RealType largestRcut_;

    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_;
    potVec longRangePot_;

    bool userChoseCutoff_;
    RealType userCutoff_;
    CutoffPolicy cutoffPolicy_;

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

  };    
}
#endif
Revision:	1576
Committed:	Wed Jun 8 16:05:07 2011 UTC (14 years, 4 months ago) by gezelter
Original Path:	*branches/development/src/parallel/ForceDecomposition.hpp*
File size:	7956 byte(s)
Log Message:	migrating cutoff information from InteractionManager to ForceManager
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
43	#define PARALLEL_FORCEDECOMPOSITION_HPP
44
45	#include "brains/SimInfo.hpp"
46	#include "brains/SnapshotManager.hpp"
47	#include "nonbonded/NonBondedInteraction.hpp"
48	#include "nonbonded/Cutoffs.hpp"
49	#include "nonbonded/InteractionManager.hpp"
50	#include "utils/Tuple.hpp"
51
52	using namespace std;
53	namespace OpenMD {
54
55	typedef tuple3<RealType, RealType, RealType> groupCutoffs;
56
57	/**
58	* @class ForceDecomposition
59	*
60	* ForceDecomposition is an interface for passing out and collecting
61	* information from many processors at various stages of the main
62	* non-bonded ForceLoop.
63	*
64	* The pairwise force calculation has an outer-running loop (the "I"
65	* loop) and an inner-running loop (the "J" loop). In parallel
66	* decompositions, these loop over different groups of atoms on
67	* different processors. Between each set of computations on the
68	* local processor, data must be exchanged among the processors.
69	* This can happen at different times in the calculation:
70	*
71	* distributeInitialData (parallel communication - one time only)
72	* distributeData (parallel communication - every ForceLoop)
73	*
74	* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
75	* \| loop over i
76	* \| \| loop over j
77	* \| \| \| localComputation
78	* \| \| end
79	* \| end
80	* \| if (nLoops > 1):
81	* \| \| collectIntermediateData (parallel communication)
82	* \| \| distributeIntermediateData (parallel communication)
83	* \| endif
84	* end
85	* collectData (parallel communication)
86	*
87	* ForceDecomposition provides the interface for ForceLoop to do the
88	* communication steps and to iterate using the correct set of atoms
89	* and cutoff groups.
90	*/
91	class ForceDecomposition {
92	public:
93
94	ForceDecomposition(SimInfo* info);
95	virtual ~ForceDecomposition() {}
96
97	virtual void distributeInitialData() = 0;
98	virtual void distributeData() = 0;
99	virtual void zeroWorkArrays() = 0;
100	virtual void collectIntermediateData() = 0;
101	virtual void distributeIntermediateData() = 0;
102	virtual void collectData() = 0;
103	virtual potVec getLongRangePotential() { return longRangePot_; }
104
105	// neighbor list routines
106	virtual bool checkNeighborList();
107	virtual vector<pair<int, int> > buildNeighborList() = 0;
108
109	// how to handle cutoffs:
110	void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
111	void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
112
113	// group bookkeeping
114	virtual groupCutoffs getGroupCutoffs(int cg1, int cg2) = 0;
115
116	// Group->atom bookkeeping
117	virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
118	virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
119
120	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
121	virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
122	virtual RealType getMassFactorRow(int atom1) = 0;
123	virtual RealType getMassFactorColumn(int atom2) = 0;
124
125	// spatial data
126	virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
127	virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
128
129	// atom bookkeeping
130	virtual int getNAtomsInRow() = 0;
131	virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
132	virtual bool skipAtomPair(int atom1, int atom2) = 0;
133	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
134	virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
135
136	// filling interaction blocks with pointers
137	virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
138	virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
139	virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
140	virtual SelfData fillSelfData(int atom1);
141
142	protected:
143	SimInfo* info_;
144	SnapshotManager* sman_;
145	Snapshot* snap_;
146	ForceField* ff_;
147	InteractionManager* interactionMan_;
148
149	int storageLayout_;
150	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
151	RealType largestRcut_;
152
153	map<pair<int, int>, int> topoDist; //< topoDist gives the
154	//topological distance between
155	//two atomic sites. This
156	//declaration is agnostic
157	//regarding the parallel
158	//decomposition. The two
159	//indices could be local or row
160	//& column. It will be up to
161	//the specific decomposition
162	//method to fill this.
163	map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
164	//to leave out of non-bonded
165	//force evaluations. This
166	//declaration is agnostic
167	//regarding the parallel
168	//decomposition. The two
169	//indices could be local or row
170	//& column. It will be up to
171	//the specific decomposition
172	//method to fill this.
173
174	vector<vector<int> > groupList_;
175
176	vector<Vector3i> cellOffsets_;
177	Vector3i nCells_;
178	vector<vector<int> > cellList_;
179	vector<Vector3d> saved_CG_positions_;
180	potVec longRangePot_;
181
182	bool userChoseCutoff_;
183	RealType userCutoff_;
184	CutoffPolicy cutoffPolicy_;
185
186	map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
187
188	};
189	}
190	#endif