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, 24107 (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_.size() > 0 ? &(pairList_[0]) : NULL;    
  }
  
  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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	5507 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			#include <functional>
44			#include <iterator>
45			#include <utility>
46
47			#include "brains/PairList.hpp"
48
49	gezelter	1390	namespace OpenMD {
50	gezelter	1288
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_.size() > 0 ? &(pairList_[0]) : NULL;
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