src/parallel/ForceDecomposition.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 "types/AtomType.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;

    virtual unsigned int getNcutoffGroupsI() = 0;
    virtual unsigned int getNcutoffGroupsJ() = 0;

    virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
    virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;

    virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
    virtual AtomType* getAtomTypeJ(int whichAtomJ) = 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:	1544
Committed:	Fri Mar 18 19:31:52 2011 UTC (14 years, 7 months ago) by gezelter
Original Path:	*branches/development/src/parallel/Decomposition.hpp*
File size:	5711 byte(s)
Log Message:	More modifications for paralllel rewrite
#	User	Rev	Content
1	gezelter	1539	/*
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	gezelter	1544	#include "brains/SimInfo.hpp"
46	gezelter	1539	#include "types/AtomType.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	gezelter	1544	*
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	gezelter	1539	* \| end
72	gezelter	1544	* \| if (nLoops > 1):
73			* \| \| collectIntermediateData (parallel communication)
74			* \| \| distributeIntermediateData (parallel communication)
75			* \| endif
76	gezelter	1539	* end
77	gezelter	1544	* collectData (parallel communication)
78	gezelter	1539	*
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	gezelter	1544	Decomposition(SimInfo* info) : info_(info) {}
87	gezelter	1539	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			virtual unsigned int getNcutoffGroupsI() = 0;
96			virtual unsigned int getNcutoffGroupsJ() = 0;
97
98			virtual vector<int> getAtomsInGroupI(int whichCGI) = 0;
99			virtual vector<int> getAtomsInGroupJ(int whichCGJ) = 0;
100
101			virtual AtomType* getAtomTypeI(int whichAtomI) = 0;
102			virtual AtomType* getAtomTypeJ(int whichAtomJ) = 0;
103
104			protected:
105	gezelter	1544	SimInfo* info_;
106			map<pair<int, int>, int> topoDist; //< topoDist gives the
107			//topological distance between
108			//two atomic sites. This
109			//declaration is agnostic
110			//regarding the parallel
111			//decomposition. The two
112			//indices could be local or row
113			//& column. It will be up to
114			//the specific decomposition
115			//method to fill this.
116			map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
117			//to leave out of non-bonded
118			//force evaluations. This
119			//declaration is agnostic
120			//regarding the parallel
121			//decomposition. The two
122			//indices could be local or row
123			//& column. It will be up to
124			//the specific decomposition
125			//method to fill this.
126	gezelter	1539	};
127			}
128			#endif