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, 234107 (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; }
    virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }

    // neighbor list routines
    virtual bool checkNeighborList();
    virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0;

    // how to handle cutoffs:
    void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
    void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }

    // group bookkeeping
    virtual void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) = 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_;
    bool usePeriodicBoundaryConditions_;
    RealType skinThickness_;   /**< Verlet neighbor list skin thickness */    
    RealType largestRcut_;

    vector<int> idents;
    vector<int> regions;
    potVec pairwisePot;
    potVec embeddingPot;
    potVec excludedPot;
    potVec excludedSelfPot;

    /** 
     * 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;
    vector<vector<RealType> > GrCut;
    vector<vector<RealType> > GrCutSq;
    vector<vector<RealType> > GrlistSq;

  };    
}
#endif
Revision:	1929
Committed:	Mon Aug 19 13:12:00 2013 UTC (11 years, 8 months ago) by gezelter
File size:	8386 byte(s)
Log Message:	Backing out fluc-rho and putting back the Electrostatic fluctuating charge with coulomb integrals for atoms within a region.
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#ifndef PARALLEL_FORCEDECOMPOSITION_HPP
44	#define PARALLEL_FORCEDECOMPOSITION_HPP
45
46	#include "brains/SimInfo.hpp"
47	#include "brains/SnapshotManager.hpp"
48	#include "nonbonded/NonBondedInteraction.hpp"
49	#include "nonbonded/Cutoffs.hpp"
50	#include "nonbonded/InteractionManager.hpp"
51	#include "utils/Tuple.hpp"
52
53	using namespace std;
54	namespace OpenMD {
55
56	typedef tuple3<RealType, RealType, RealType> groupCutoffs;
57
58	/**
59	* @class ForceDecomposition
60	*
61	* 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	* 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	*
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	* \| end
81	* \| if (nLoops > 1):
82	* \| \| collectIntermediateData (parallel communication)
83	* \| \| distributeIntermediateData (parallel communication)
84	* \| endif
85	* end
86	* collectData (parallel communication)
87	* loop over i
88	* \| localComputation
89	* end
90	* collectSelfData (parallel communication)
91	*
92	* ForceDecomposition provides the interface for ForceLoop to do the
93	* communication steps and to iterate using the correct set of atoms
94	* and cutoff groups.
95	*/
96	class ForceDecomposition {
97	public:
98
99	ForceDecomposition(SimInfo* info, InteractionManager* iMan);
100	virtual ~ForceDecomposition() {}
101
102	virtual void distributeInitialData() = 0;
103	virtual void distributeData() = 0;
104	virtual void zeroWorkArrays() = 0;
105	virtual void collectIntermediateData() = 0;
106	virtual void distributeIntermediateData() = 0;
107	virtual void collectData() = 0;
108	virtual void collectSelfData() = 0;
109	virtual potVec* getEmbeddingPotential() { return &embeddingPot; }
110	virtual potVec* getPairwisePotential() { return &pairwisePot; }
111	virtual potVec* getExcludedPotential() { return &excludedPot; }
112	virtual potVec* getExcludedSelfPotential() { return &excludedSelfPot; }
113
114	// neighbor list routines
115	virtual bool checkNeighborList();
116	virtual void buildNeighborList(vector<pair<int, int> >& neighborList) = 0;
117
118	// how to handle cutoffs:
119	void setCutoffPolicy(CutoffPolicy cp) {cutoffPolicy_ = cp;}
120	void setUserCutoff(RealType rcut) {userCutoff_ = rcut; userChoseCutoff_ = true; }
121
122	// group bookkeeping
123	virtual void getGroupCutoffs(int &cg1, int &cg2, RealType &rcut, RealType &rcutsq, RealType &rlistsq) = 0;
124	virtual Vector3d& getGroupVelocityColumn(int atom2) = 0;
125
126	// Group->atom bookkeeping
127	virtual vector<int>& getAtomsInGroupRow(int cg1) = 0;
128	virtual vector<int>& getAtomsInGroupColumn(int cg2) = 0;
129
130	virtual Vector3d getAtomToGroupVectorRow(int atom1, int cg1) = 0;
131	virtual Vector3d getAtomToGroupVectorColumn(int atom2, int cg2) = 0;
132	virtual RealType& getMassFactorRow(int atom1) = 0;
133	virtual RealType& getMassFactorColumn(int atom2) = 0;
134
135	// spatial data
136	virtual Vector3d getIntergroupVector(int cg1, int cg2) = 0;
137	virtual Vector3d getInteratomicVector(int atom1, int atom2) = 0;
138
139	// atom bookkeeping
140	virtual int& getNAtomsInRow() = 0;
141	virtual vector<int>& getExcludesForAtom(int atom1) = 0;
142	virtual bool skipAtomPair(int atom1, int atom2, int cg1, int cg2) = 0;
143	virtual bool excludeAtomPair(int atom1, int atom2) = 0;
144	virtual int getTopologicalDistance(int atom1, int atom2) = 0;
145	virtual void addForceToAtomRow(int atom1, Vector3d fg) = 0;
146	virtual void addForceToAtomColumn(int atom2, Vector3d fg) = 0;
147	virtual Vector3d& getAtomVelocityColumn(int atom2) = 0;
148
149	// filling interaction blocks with pointers
150	virtual void fillInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
151	virtual void unpackInteractionData(InteractionData &idat, int atom1, int atom2) = 0;
152
153	virtual void fillSelfData(SelfData &sdat, int atom1);
154
155	virtual void addToHeatFlux(Vector3d hf);
156	virtual void setHeatFlux(Vector3d hf);
157
158	protected:
159	SimInfo* info_;
160	SnapshotManager* sman_;
161	Snapshot* snap_;
162	ForceField* ff_;
163	InteractionManager* interactionMan_;
164
165	int storageLayout_;
166	bool needVelocities_;
167	bool usePeriodicBoundaryConditions_;
168	RealType skinThickness_; /*< Verlet neighbor list skin thickness /
169	RealType largestRcut_;
170
171	vector<int> idents;
172	vector<int> regions;
173	potVec pairwisePot;
174	potVec embeddingPot;
175	potVec excludedPot;
176	potVec excludedSelfPot;
177
178	/**
179	* The topological distance between two atomic sites is handled
180	* via two vector structures for speed. These structures agnostic
181	* regarding the parallel decomposition. The index for
182	* toposForAtom could be local or row, while the values could be
183	* local or column. It will be up to the specific decomposition
184	* method to fill these.
185	*/
186	vector<vector<int> > toposForAtom;
187	vector<vector<int> > topoDist;
188	vector<vector<int> > excludesForAtom;
189	vector<vector<int> > groupList_;
190	vector<RealType> massFactors;
191	vector<AtomType*> atypesLocal;
192
193	vector<Vector3i> cellOffsets_;
194	Vector3i nCells_;
195	vector<vector<int> > cellList_;
196	vector<Vector3d> saved_CG_positions_;
197
198	bool userChoseCutoff_;
199	RealType userCutoff_;
200	CutoffPolicy cutoffPolicy_;
201
202	//map<pair<int, int>, tuple3<RealType, RealType, RealType> > gTypeCutoffMap;
203	vector<vector<RealType> > GrCut;
204	vector<vector<RealType> > GrCutSq;
205	vector<vector<RealType> > GrlistSq;
206
207	};
208	}
209	#endif