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, 24107 (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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	3911 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1288	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	1288	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	1288	* 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	gezelter	1390	*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1288	*/
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	gezelter	1390	namespace OpenMD {
53	gezelter	1288
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	gezelter	1545	* lists.
60	gezelter	1288	*/
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	gezelter	1390	} //end namespace OpenMD
104	gezelter	1288
105			#endif // __PAIRLIST_H__