src/brains/PairList.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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#ifndef BRAINS_PAIRLIST_HPP

#define BRAINS_PAIRLIST_HPP

#include <iostream>
#include <set>
#include <utility>
#include <vector>

namespace oopse {

  /**
   * @class PairList PairList.hpp "brains/PairList.hpp"
   * @brief PairList class maintains a general purpose list of atom
   * pairs using the global indices of the atoms.  This structure is
   * the general form for exclude lists as well as 1-4, 1-3, and 1-2 
   * lists.  The PairLists are passed to fortran in a plain array.
   */
  class PairList {
  public:

    PairList() : modified_(false) {}


    /** Adds a pair into this PairList class */
    void addPair(int i, int j);

    void addPairs(std::set<int>& set1, std::set<int>& set2);
    template<typename IterType1, typename IterType2>
    void addPairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);

    /** Remove a pair from PairList class */
    void removePair(int i, int j);

    void removePairs(std::set<int>& set1, std::set<int>& set2);
    template<typename IterType1, typename IterType2>
    void removePairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);

    /** Checks whether pair (i, j) is in this PairList class */
    bool hasPair(int i, int j);

    /** Returns the number of pairs in the list */
    int getSize();

    /** Returns the size of PairList */
    int getSizeOfPairList();

    /** Returns the pairs in a plain array*/
    int *getPairList();

    /** write out the exclusion list to an ostream */
    friend std::ostream& operator <<(std::ostream& o, PairList& e);

  private:

    std::set < std::pair<int, int> > pairSet_;
    std::vector <int> pairList_;
    bool modified_;
  };

}      //end namespace oopse

#endif // __PAIRLIST_H__
Revision:	3443
Committed:	Wed Sep 10 18:13:35 2008 UTC (15 years, 9 months ago) by gezelter
File size:	3857 byte(s)
Log Message:	Exclude is gone. Replaced by a generic PairList to handle 1-2, 1-3, and 1-4 interactions as well as the exclude list
#	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. Acknowledgement of the program authors must be made in any
10	* publication of scientific results based in part on use of the
11	* program. An acceptable form of acknowledgement is citation of
12	* the article in which the program was described (Matthew
13	* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	* Parallel Simulation Engine for Molecular Dynamics,"
16	* J. Comput. Chem. 26, pp. 252-271 (2005))
17	*
18	* 2. Redistributions of source code must retain the above copyright
19	* notice, this list of conditions and the following disclaimer.
20	*
21	* 3. Redistributions in binary form must reproduce the above copyright
22	* notice, this list of conditions and the following disclaimer in the
23	* documentation and/or other materials provided with the
24	* distribution.
25	*
26	* This software is provided "AS IS," without a warranty of any
27	* kind. All express or implied conditions, representations and
28	* warranties, including any implied warranty of merchantability,
29	* fitness for a particular purpose or non-infringement, are hereby
30	* excluded. The University of Notre Dame and its licensors shall not
31	* be liable for any damages suffered by licensee as a result of
32	* using, modifying or distributing the software or its
33	* derivatives. In no event will the University of Notre Dame or its
34	* licensors be liable for any lost revenue, profit or data, or for
35	* direct, indirect, special, consequential, incidental or punitive
36	* damages, however caused and regardless of the theory of liability,
37	* arising out of the use of or inability to use software, even if the
38	* University of Notre Dame has been advised of the possibility of
39	* such damages.
40	*/
41
42	#ifndef BRAINS_PAIRLIST_HPP
43
44	#define BRAINS_PAIRLIST_HPP
45
46	#include <iostream>
47	#include <set>
48	#include <utility>
49	#include <vector>
50
51	namespace oopse {
52
53	/**
54	* @class PairList PairList.hpp "brains/PairList.hpp"
55	* @brief PairList class maintains a general purpose list of atom
56	* pairs using the global indices of the atoms. This structure is
57	* the general form for exclude lists as well as 1-4, 1-3, and 1-2
58	* lists. The PairLists are passed to fortran in a plain array.
59	*/
60	class PairList {
61	public:
62
63	PairList() : modified_(false) {}
64
65
66	/** Adds a pair into this PairList class */
67	void addPair(int i, int j);
68
69	void addPairs(std::set<int>& set1, std::set<int>& set2);
70	template<typename IterType1, typename IterType2>
71	void addPairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);
72
73	/** Remove a pair from PairList class */
74	void removePair(int i, int j);
75
76	void removePairs(std::set<int>& set1, std::set<int>& set2);
77	template<typename IterType1, typename IterType2>
78	void removePairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);
79
80	/** Checks whether pair (i, j) is in this PairList class */
81	bool hasPair(int i, int j);
82
83	/** Returns the number of pairs in the list */
84	int getSize();
85
86	/** Returns the size of PairList */
87	int getSizeOfPairList();
88
89	/** Returns the pairs in a plain array*/
90	int *getPairList();
91
92	/** write out the exclusion list to an ostream */
93	friend std::ostream& operator <<(std::ostream& o, PairList& e);
94
95	private:
96
97	std::set < std::pair<int, int> > pairSet_;
98	std::vector <int> pairList_;
99	bool modified_;
100	};
101
102	} //end namespace oopse
103
104	#endif // __PAIRLIST_H__