src/brains/PairList.cpp

/*
 * 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).
 */
 
#include <functional>
#include <iterator>
#include <utility>

#include "brains/PairList.hpp"

namespace OpenMD {
  
  int *PairList::getPairList() {

    if (modified_) {
      pairList_.clear();
      
      for (std::set<std::pair<int,int> >::iterator i = pairSet_.begin();
           i != pairSet_.end(); ++i) {
        pairList_.push_back(i->first + 1);
        pairList_.push_back(i->second + 1);            
      }
      modified_ = false;
    } 
    
    return pairList_.empty() ? NULL : &(pairList_[0]);
  }
  
  void PairList::addPair(int i, int j) {
    
    if (i == j) {
      return;
    } else if (i > j) {
      std::swap(i, j);
    }
    
    std::set<std::pair<int, int> >::iterator iter = pairSet_.find(std::make_pair(i, j));
    
    if (iter == pairSet_.end()) {
      pairSet_.insert(std::make_pair(i, j));
      modified_ = true;
    }
  }
  
  void PairList::addPairs(std::set<int>& set1, std::set<int>& set2) {
    for (std::set<int>::iterator iter1 = set1.begin(); 
         iter1 !=  set1.end(); ++ iter1) {
      for(std::set<int>::iterator iter2 = set2.begin(); 
          iter2 != set2.end(); ++ iter2) {
        this->addPair(*iter1, *iter2);
      }
    }    
  }

  template<typename IterType1, typename IterType2>
  void PairList::addPairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last) {
    for (IterType1 iter1 = iter1_first; iter1 != iter1_last; ++ iter1) {
      for(IterType2 iter2 = iter2_first; iter2 != iter2_last; ++ iter2) {
        this->addPair(*iter1, * iter2);
      }
    }
  }

  void PairList::removePair(int i, int j) {    
    if (i == j) {
      return;
    } else if (i > j) {
      std::swap(i, j);
    }


    std::set<std::pair<int, int> >::iterator iter = pairSet_.find(std::make_pair(i, j));
    
    if (iter != pairSet_.end()) {
      pairSet_.erase(iter);
      modified_ = true;
    }
  }

  void PairList::removePairs(std::set<int>& set1, std::set<int>& set2) {
    for (std::set<int>::iterator iter1 = set1.begin(); 
         iter1 !=  set1.end(); ++ iter1) {
      for(std::set<int>::iterator iter2 = set2.begin(); 
          iter2 != set2.end(); ++ iter2) {
        this->removePair(*iter1, * iter2);
      }
    }    
  }

  template<typename IterType1, typename IterType2>
  void PairList::removePairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last) {
    for (IterType1 iter1 = iter1_first; iter1 != iter1_last; ++ iter1) {
      for(IterType2 iter2 = iter2_first; iter2 != iter2_last; ++ iter2) {
        this->removePair(*iter1, * iter2);
      }
    }
  }

  bool PairList::hasPair(int i, int j) {
    
    if (i == j) {
      return false;
    } else if (i > j) {
      std::swap(i, j);
    }
    
    std::set<std::pair<int, int> >::iterator  iter = pairSet_.find(std::make_pair(i, j));
    return iter == pairSet_.end() ? false : true; 
  }
  
  int PairList::getSize() {
    return pairSet_.size();
  }

  std::ostream& operator <<(std::ostream& o, PairList& e) {
    std::set<std::pair<int, int> >::iterator i;
    
    int index;
    
    index = 0;
    
    for(i = e.pairSet_.begin(); i != e.pairSet_.end(); ++i) {
      o << "pairList[" << index << "] i, j: " << (*i).first << " - "
        << (*i).second << "\n";
      index++;
    }
    
    return o;
  }
  
}

  
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	5501 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	#include <functional>
44	#include <iterator>
45	#include <utility>
46
47	#include "brains/PairList.hpp"
48
49	namespace OpenMD {
50
51	int *PairList::getPairList() {
52
53	if (modified_) {
54	pairList_.clear();
55
56	for (std::set<std::pair<int,int> >::iterator i = pairSet_.begin();
57	i != pairSet_.end(); ++i) {
58	pairList_.push_back(i->first + 1);
59	pairList_.push_back(i->second + 1);
60	}
61	modified_ = false;
62	}
63
64	return pairList_.empty() ? NULL : &(pairList_[0]);
65	}
66
67	void PairList::addPair(int i, int j) {
68
69	if (i == j) {
70	return;
71	} else if (i > j) {
72	std::swap(i, j);
73	}
74
75	std::set<std::pair<int, int> >::iterator iter = pairSet_.find(std::make_pair(i, j));
76
77	if (iter == pairSet_.end()) {
78	pairSet_.insert(std::make_pair(i, j));
79	modified_ = true;
80	}
81	}
82
83	void PairList::addPairs(std::set<int>& set1, std::set<int>& set2) {
84	for (std::set<int>::iterator iter1 = set1.begin();
85	iter1 != set1.end(); ++ iter1) {
86	for(std::set<int>::iterator iter2 = set2.begin();
87	iter2 != set2.end(); ++ iter2) {
88	this->addPair(iter1, iter2);
89	}
90	}
91	}
92
93	template<typename IterType1, typename IterType2>
94	void PairList::addPairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last) {
95	for (IterType1 iter1 = iter1_first; iter1 != iter1_last; ++ iter1) {
96	for(IterType2 iter2 = iter2_first; iter2 != iter2_last; ++ iter2) {
97	this->addPair(iter1, iter2);
98	}
99	}
100	}
101
102	void PairList::removePair(int i, int j) {
103	if (i == j) {
104	return;
105	} else if (i > j) {
106	std::swap(i, j);
107	}
108
109
110	std::set<std::pair<int, int> >::iterator iter = pairSet_.find(std::make_pair(i, j));
111
112	if (iter != pairSet_.end()) {
113	pairSet_.erase(iter);
114	modified_ = true;
115	}
116	}
117
118	void PairList::removePairs(std::set<int>& set1, std::set<int>& set2) {
119	for (std::set<int>::iterator iter1 = set1.begin();
120	iter1 != set1.end(); ++ iter1) {
121	for(std::set<int>::iterator iter2 = set2.begin();
122	iter2 != set2.end(); ++ iter2) {
123	this->removePair(iter1, iter2);
124	}
125	}
126	}
127
128	template<typename IterType1, typename IterType2>
129	void PairList::removePairs(IterType1 iter1_first, IterType1 iter1_last, IterType2 iter2_first, IterType2 iter2_last) {
130	for (IterType1 iter1 = iter1_first; iter1 != iter1_last; ++ iter1) {
131	for(IterType2 iter2 = iter2_first; iter2 != iter2_last; ++ iter2) {
132	this->removePair(iter1, iter2);
133	}
134	}
135	}
136
137	bool PairList::hasPair(int i, int j) {
138
139	if (i == j) {
140	return false;
141	} else if (i > j) {
142	std::swap(i, j);
143	}
144
145	std::set<std::pair<int, int> >::iterator iter = pairSet_.find(std::make_pair(i, j));
146	return iter == pairSet_.end() ? false : true;
147	}
148
149	int PairList::getSize() {
150	return pairSet_.size();
151	}
152
153	std::ostream& operator <<(std::ostream& o, PairList& e) {
154	std::set<std::pair<int, int> >::iterator i;
155
156	int index;
157
158	index = 0;
159
160	for(i = e.pairSet_.begin(); i != e.pairSet_.end(); ++i) {
161	o << "pairList[" << index << "] i, j: " << (*i).first << " - "
162	<< (*i).second << "\n";
163	index++;
164	}
165
166	return o;
167	}
168
169	}
170
171