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"

using namespace std;
namespace OpenMD {
  
  /**
   * @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;

    // group bookkeeping
    virtual pair<int, int> getGroupTypes(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_;
    int storageLayout_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    

    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_;

  };    
}
#endif
Revision:	1575
Committed:	Fri Jun 3 21:39:49 2011 UTC (13 years, 10 months ago) by gezelter
File size:	7373 byte(s)
Log Message:	more parallel fixes
#	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
49	using namespace std;
50	namespace OpenMD {
51
52	/**
53	* @class ForceDecomposition
54	*
55	* ForceDecomposition is an interface for passing out and collecting
56	* information from many processors at various stages of the main
57	* non-bonded ForceLoop.
58	*
59	* The pairwise force calculation has an outer-running loop (the "I"
60	* loop) and an inner-running loop (the "J" loop). In parallel
61	* decompositions, these loop over different groups of atoms on
62	* different processors. Between each set of computations on the
63	* local processor, data must be exchanged among the processors.
64	* This can happen at different times in the calculation:
65	*
66	* distributeInitialData (parallel communication - one time only)
67	* distributeData (parallel communication - every ForceLoop)
68	*
69	* loop iLoop over nLoops (nLoops may be 1, 2, or until self consistent)
70	* \| loop over i
71	* \| \| loop over j
72	* \| \| \| localComputation
73	* \| \| end
74	* \| end
75	* \| if (nLoops > 1):
76	* \| \| collectIntermediateData (parallel communication)
77	* \| \| distributeIntermediateData (parallel communication)
78	* \| endif
79	* end
80	* collectData (parallel communication)
81	*
82	* ForceDecomposition provides the interface for ForceLoop to do the
83	* communication steps and to iterate using the correct set of atoms
84	* and cutoff groups.
85	*/
86	class ForceDecomposition {
87	public:
88
89	ForceDecomposition(SimInfo* info);
90	virtual ~ForceDecomposition() {}
91
92	virtual void distributeInitialData() = 0;
93	virtual void distributeData() = 0;
94	virtual void zeroWorkArrays() = 0;
95	virtual void collectIntermediateData() = 0;
96	virtual void distributeIntermediateData() = 0;
97	virtual void collectData() = 0;
98	virtual potVec getLongRangePotential() { return longRangePot_; }
99
100	// neighbor list routines
101	virtual bool checkNeighborList();
102	virtual vector<pair<int, int> > buildNeighborList() = 0;
103
104	// group bookkeeping
105	virtual pair<int, int> getGroupTypes(int cg1, int cg2) = 0;
106
107	// Group->atom bookkeeping
108	virtual vector<int> getAtomsInGroupRow(int cg1) = 0;
109	virtual vector<int> getAtomsInGroupColumn(int cg2) = 0;
110
111	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
112	virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
113	virtual RealType getMassFactorRow(int atom1) = 0;
114	virtual RealType getMassFactorColumn(int atom2) = 0;
115
116	// spatial data
117	virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
118	virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
119
120	// atom bookkeeping
121	virtual int getNAtomsInRow() = 0;
122	virtual vector<int> getSkipsForRowAtom(int atom1) = 0;
123	virtual bool skipAtomPair(int atom1, int atom2) = 0;
124	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
125	virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
126
127	// filling interaction blocks with pointers
128	virtual InteractionData fillInteractionData(int atom1, int atom2) = 0;
129	virtual void unpackInteractionData(InteractionData idat, int atom1, int atom2) = 0;
130	virtual InteractionData fillSkipData(int atom1, int atom2) = 0;
131	virtual SelfData fillSelfData(int atom1);
132
133	protected:
134	SimInfo* info_;
135	SnapshotManager* sman_;
136	Snapshot* snap_;
137	ForceField* ff_;
138	int storageLayout_;
139	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
140
141	map<pair<int, int>, int> topoDist; //< topoDist gives the
142	//topological distance between
143	//two atomic sites. This
144	//declaration is agnostic
145	//regarding the parallel
146	//decomposition. The two
147	//indices could be local or row
148	//& column. It will be up to
149	//the specific decomposition
150	//method to fill this.
151	map<pair<int, int>, bool> exclude; //< exclude is the set of pairs
152	//to leave out of non-bonded
153	//force evaluations. This
154	//declaration is agnostic
155	//regarding the parallel
156	//decomposition. The two
157	//indices could be local or row
158	//& column. It will be up to
159	//the specific decomposition
160	//method to fill this.
161
162	vector<vector<int> > groupList_;
163	vector<Vector3i> cellOffsets_;
164	Vector3i nCells_;
165	vector<vector<int> > cellList_;
166	vector<Vector3d> saved_CG_positions_;
167	potVec longRangePot_;
168
169	};
170	}
171	#endif