src/parallel/Decomposition.hpp

/*
 * Copyright (c) 2005 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_DECOMPOSITION_HPP
#define PARALLEL_DECOMPOSITION_HPP

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

using namespace std;
namespace OpenMD {
  
  /**
   * @class Decomposition 
   * Decomposition 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)
   *
   * Decomposition provides the interface for ForceLoop to do the
   * communication steps and to iterate using the correct set of atoms
   * and cutoff groups.
   */
  class Decomposition {
  public:

    Decomposition(SimInfo* info) : info_(info) {}
    virtual ~Decomposition() {}
    
    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() = 0;
    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> getAtomsInGroupI(int cg1) = 0;
    virtual vector<int> getAtomsInGroupJ(int cg2) = 0;
    virtual Vector3d getAtomToGroupVectorI(int atom1, int cg1) = 0;
    virtual Vector3d getAtomToGroupVectorJ(int atom2, int cg2) = 0;
    virtual RealType getMfactI(int atom1) = 0;
    virtual RealType getMfactJ(int atom2) = 0;

    // spatial data
    virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
    virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
       
    // atom bookkeeping
    virtual vector<int> getAtomList() = 0;
    virtual vector<int> getSkipsForAtom(int atom1) = 0;
    virtual bool skipAtomPair(int atom1, int atom2) = 0;
    virtual void addForceToAtomI(int atom1, Vector3d fg) = 0;
    virtual void addForceToAtomJ(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) = 0;
    
  protected:
    SimInfo* info_;   
    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.
  };    
}
#endif
Revision:	1546
Committed:	Sun Apr 10 15:16:39 2011 UTC (14 years ago) by gezelter
File size:	6697 byte(s)
Log Message:	closer to a real force loop
#	Content
1	/*
2	* Copyright (c) 2005 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_DECOMPOSITION_HPP
43	#define PARALLEL_DECOMPOSITION_HPP
44
45	#include "brains/SimInfo.hpp"
46	#include "nonbonded/NonBondedInteraction.hpp"
47
48	using namespace std;
49	namespace OpenMD {
50
51	/**
52	* @class Decomposition
53	* Decomposition is an interface for passing out and collecting information
54	* from many processors at various stages of the main non-bonded ForceLoop.
55	*
56	* The pairwise force calculation has an outer-running loop (the "I"
57	* loop) and an inner-running loop (the "J" loop). In parallel
58	* decompositions, these loop over different groups of atoms on
59	* different processors. Between each set of computations on the
60	* local processor, data must be exchanged among the processors.
61	* This can happen at different times in the calculation:
62	*
63	* distributeInitialData (parallel communication - one time only)
64	* distributeData (parallel communication - every ForceLoop)
65	*
66	* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
67	* \| loop over i
68	* \| \| loop over j
69	* \| \| \| localComputation
70	* \| \| end
71	* \| end
72	* \| if (nLoops > 1):
73	* \| \| collectIntermediateData (parallel communication)
74	* \| \| distributeIntermediateData (parallel communication)
75	* \| endif
76	* end
77	* collectData (parallel communication)
78	*
79	* Decomposition provides the interface for ForceLoop to do the
80	* communication steps and to iterate using the correct set of atoms
81	* and cutoff groups.
82	*/
83	class Decomposition {
84	public:
85
86	Decomposition(SimInfo* info) : info_(info) {}
87	virtual ~Decomposition() {}
88
89	virtual void distributeInitialData() = 0;
90	virtual void distributeData() = 0;
91	virtual void collectIntermediateData() = 0;
92	virtual void distributeIntermediateData() = 0;
93	virtual void collectData() = 0;
94
95	// neighbor list routines
96	virtual bool checkNeighborList() = 0;
97	virtual vector<pair<int, int> > buildNeighborList() = 0;
98
99	// group bookkeeping
100	virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
101
102	// Group->atom bookkeeping
103	virtual vector<int> getAtomsInGroupI(int cg1) = 0;
104	virtual vector<int> getAtomsInGroupJ(int cg2) = 0;
105	virtual Vector3d getAtomToGroupVectorI(int atom1, int cg1) = 0;
106	virtual Vector3d getAtomToGroupVectorJ(int atom2, int cg2) = 0;
107	virtual RealType getMfactI(int atom1) = 0;
108	virtual RealType getMfactJ(int atom2) = 0;
109
110	// spatial data
111	virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
112	virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
113
114	// atom bookkeeping
115	virtual vector<int> getAtomList() = 0;
116	virtual vector<int> getSkipsForAtom(int atom1) = 0;
117	virtual bool skipAtomPair(int atom1, int atom2) = 0;
118	virtual void addForceToAtomI(int atom1, Vector3d fg) = 0;
119	virtual void addForceToAtomJ(int atom2, Vector3d fg) = 0;
120
121	// filling interaction blocks with pointers
122	virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
123	virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
124	virtual SelfData fillSelfData(int atom1) = 0;
125
126	protected:
127	SimInfo* info_;
128	map<pair<int, int>, int> topoDist; //< topoDist gives the
129	//topological distance between
130	//two atomic sites. This
131	//declaration is agnostic
132	//regarding the parallel
133	//decomposition. The two
134	//indices could be local or row
135	//& column. It will be up to
136	//the specific decomposition
137	//method to fill this.
138	map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
139	//to leave out of non-bonded
140	//force evaluations. This
141	//declaration is agnostic
142	//regarding the parallel
143	//decomposition. The two
144	//indices could be local or row
145	//& column. It will be up to
146	//the specific decomposition
147	//method to fill this.
148	};
149	}
150	#endif