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. 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 BRAINS_PAIRLIST_HPP

#define BRAINS_PAIRLIST_HPP

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

namespace OpenMD {

  /**
   * @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.
   */
  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 OpenMD

#endif // __PAIRLIST_H__
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 2 months ago) by gezelter
File size:	3912 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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, 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 BRAINS_PAIRLIST_HPP
44
45	#define BRAINS_PAIRLIST_HPP
46
47	#include <iostream>
48	#include <set>
49	#include <utility>
50	#include <vector>
51
52	namespace OpenMD {
53
54	/**
55	* @class PairList PairList.hpp "brains/PairList.hpp"
56	* @brief PairList class maintains a general purpose list of atom
57	* pairs using the global indices of the atoms. This structure is
58	* the general form for exclude lists as well as 1-4, 1-3, and 1-2
59	* lists.
60	*/
61	class PairList {
62	public:
63
64	PairList() : modified_(false) {}
65
66
67	/** Adds a pair into this PairList class */
68	void addPair(int i, int j);
69
70	void addPairs(std::set<int>& set1, std::set<int>& set2);
71	template<typename IterType1, typename IterType2>
72	void addPairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);
73
74	/** Remove a pair from PairList class */
75	void removePair(int i, int j);
76
77	void removePairs(std::set<int>& set1, std::set<int>& set2);
78	template<typename IterType1, typename IterType2>
79	void removePairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last);
80
81	/** Checks whether pair (i, j) is in this PairList class */
82	bool hasPair(int i, int j);
83
84	/** Returns the number of pairs in the list */
85	int getSize();
86
87	/** Returns the size of PairList */
88	int getSizeOfPairList();
89
90	/** Returns the pairs in a plain array*/
91	int *getPairList();
92
93	/** write out the exclusion list to an ostream */
94	friend std::ostream& operator <<(std::ostream& o, PairList& e);
95
96	private:
97
98	std::set < std::pair<int, int> > pairSet_;
99	std::vector <int> pairList_;
100	bool modified_;
101	};
102
103	} //end namespace OpenMD
104
105	#endif // __PAIRLIST_H__