src/utils/LocalIndexManager.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).
 */
 
/**
 * @file LocalIndexManager.hpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */ 

#ifndef UTILS_LOCALINDEXMANAGER_HPP
#define UTILS_LOCALINDEXMANAGER_HPP
#include <algorithm>
#include <iostream>
#include <cassert>
#include <list>
#include <utility>

namespace OpenMD {

  /**
   * @class IndexListContainer
   * @brief 
   * @todo documentation
   */
  class IndexListContainer{
  public:
    static const int MAX_INTEGER = 2147483647;
    typedef std::list<std::pair<int, int> >::iterator  IndexListContainerIterator;

        
    IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER) 
      :minIndex_(minIndex), maxIndex_(maxIndex) {
            
        indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
      }
        
    int pop() {
            
      if (indexContainer_.empty()) {
        std::cerr << "" << std::endl;
      }

      int result;
            
      result = indexContainer_.front().first;
            
      if (indexContainer_.front().first  == indexContainer_.front().second) {
        indexContainer_.pop_front();
      } else if (indexContainer_.front().first < indexContainer_.front().second) {
        ++indexContainer_.front().first;
      } else {
        std::cerr << "" << std::endl;
      }

      return result;
    }


    /**
     *
     */
    void insert(int index) {
      IndexListContainerIterator insertPos = internalInsert(index, index);            
      merge(insertPos);
    }

    /**
     * Reclaims an index range
     * @param beginIndex
     * @param endIndex
     */
    void insert(int beginIndex, int endIndex) {
      IndexListContainerIterator insertPos = internalInsert(beginIndex, endIndex); 
      merge(insertPos);            
    }

    /**
     * Reclaims an index array.
     * @param indices
     */
    void insert(std::vector<int>& indices){

      if (indices.empty()) {
        return;
      }
            
      std::sort(indices.begin(), indices.end());
      std::unique(indices.begin(), indices.end());

      std::vector<int>::iterator i;
      int beginIndex;

      beginIndex = indices[0];
        
      for ( i = indices.begin() + 1 ; i != indices.end(); ++i) {
        if (*i != *(i -1) + 1) {
          insert(beginIndex, *(i-1));
          beginIndex = *i;
        }
      }
    }
        
    std::vector<int> getIndicesBefore(int index) {
      std::vector<int> result;
      IndexListContainerIterator i;

      for(i = indexContainer_.begin(); i != indexContainer_.end(); ++i) {
        if ((*i).first > index) {
          //we locate the node whose minimum index is greater that index
          indexContainer_.erase(indexContainer_.begin(), i);
          break;
        } else if ((*i).second < index) {
          //The biggest index current node hold is less than the index we want
          for (int j = (*i).first; j <= (*i).second; ++j) {
            result.push_back(j);
          }
          continue;
        } else if ((*i).first == (*i).second) {
          //the index happen to equal to a node which only contains one index
          result.push_back((*i).first);
          indexContainer_.erase(indexContainer_.begin(), i);
          break;
        } else {

          for (int j = (*i).first; j < index; ++j) {
            result.push_back(j);
          }
                        
          (*i).first =  index;                   
          indexContainer_.erase(indexContainer_.begin(), i);
          break;
        }
                
      }

      return result;

    }
        
    int getMaxIndex() {
      return maxIndex_;
    }
                
  private:
        
    IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {

      if (beginIndex > endIndex) {
        std::swap(beginIndex, endIndex);
        std::cerr << "" << std::endl;
      }

      if (endIndex > maxIndex_) {
        std::cerr << "" << std::endl;
      }
      
      IndexListContainerIterator i = indexContainer_.begin();  
      for (; i != indexContainer_.end(); ++i) {
        if ((*i).first > endIndex) {
          indexContainer_.insert(i, std::make_pair(beginIndex, endIndex));
          return --i;
        } else if ((*i).second < beginIndex) {
          continue;
        } else {
          std::cerr << "" << std::endl;
        }
      }

      indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
      return --indexContainer_.end();

    }

    void merge(IndexListContainerIterator i) {
      IndexListContainerIterator j;

      //check whether current node can be merged with its previous node            
      if ( i != indexContainer_.begin()) {
        j = i;
        --j;
        if (j != indexContainer_.begin() && (*j).second + 1 == (*i).first) {
          (*i).first = (*j).first;
          indexContainer_.erase(j);
        }
      }

      //check whether current node can be merged with its next node            
      if ( i != indexContainer_.end()) {
        j = i;
        ++j;

        if (j != indexContainer_.end() && (*i).second + 1 == (*j).first) {
          (*i).second = (*j).second;
          indexContainer_.erase(j);
        }
      }

    }
    int minIndex_;
    int maxIndex_;        
    std::list<std::pair<int, int> > indexContainer_;
  };


  /**
   * @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
   * @brief
   */
  class LocalIndexManager {
  public:
        
    int getNextAtomIndex() {
      return atomIndexContainer_.pop();
    }

    std::vector<int> getAtomIndicesBefore(int index) {
      return atomIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseAtomIndex(int index) {
      atomIndexContainer_.insert(index);
    }

    void releaseAtomIndex(int beginIndex, int endIndex) {
      atomIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseAtomIndex(std::vector<int> indices) {
      atomIndexContainer_.insert(indices);
    }

    int getNextRigidBodyIndex() {
      return rigidBodyIndexContainer_.pop();
    }

    std::vector<int> getRigidBodyIndicesBefore(int index) {
      return rigidBodyIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseRigidBodyIndex(int index) {
      rigidBodyIndexContainer_.insert(index);
    }

    void releaseRigidBodyIndex(int beginIndex, int endIndex) {
      rigidBodyIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseRigidBodyIndex(std::vector<int> indices) {
      rigidBodyIndexContainer_.insert(indices);
    }

    int getNextCutoffGroupIndex() {
      return cutoffGroupIndexContainer_.pop();
    }

    std::vector<int> getCutoffGroupIndicesBefore(int index) {
      return cutoffGroupIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseCutoffGroupIndex(int index) {
      cutoffGroupIndexContainer_.insert(index);
    }

    void releaseCutoffGroupIndex(int beginIndex, int endIndex) {
      cutoffGroupIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseCutoffGroupIndex(std::vector<int> indices) {
      cutoffGroupIndexContainer_.insert(indices);
    }
 
  private:

    IndexListContainer atomIndexContainer_;
    IndexListContainer rigidBodyIndexContainer_;
    IndexListContainer cutoffGroupIndexContainer_;
  };

} //end namespace OpenMD
#endif //UTILS_LOCALINDEXMANAGER_HPP
Revision:	1874
Committed:	Wed May 15 15:09:35 2013 UTC (11 years, 11 months ago) by gezelter
File size:	9084 byte(s)
Log Message:	Fixed a bunch of cppcheck warnings.
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	246	* 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	246	* 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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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	246	*/
42
43			/**
44			* @file LocalIndexManager.hpp
45			* @author tlin
46			* @date 11/02/2004
47			* @version 1.0
48			*/
49
50			#ifndef UTILS_LOCALINDEXMANAGER_HPP
51			#define UTILS_LOCALINDEXMANAGER_HPP
52			#include <algorithm>
53			#include <iostream>
54			#include <cassert>
55			#include <list>
56			#include <utility>
57
58	gezelter	1390	namespace OpenMD {
59	gezelter	246
60	gezelter	507	/**
61			* @class IndexListContainer
62			* @brief
63			* @todo documentation
64			*/
65			class IndexListContainer{
66			public:
67			static const int MAX_INTEGER = 2147483647;
68			typedef std::list<std::pair<int, int> >::iterator IndexListContainerIterator;
69	gezelter	246
70
71	gezelter	507	IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER)
72			:minIndex_(minIndex), maxIndex_(maxIndex) {
73	gezelter	246
74	gezelter	507	indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
75			}
76	gezelter	246
77	gezelter	507	int pop() {
78	gezelter	246
79	gezelter	507	if (indexContainer_.empty()) {
80			std::cerr << "" << std::endl;
81			}
82	gezelter	246
83	gezelter	507	int result;
84	gezelter	246
85	gezelter	507	result = indexContainer_.front().first;
86	gezelter	246
87	gezelter	507	if (indexContainer_.front().first == indexContainer_.front().second) {
88			indexContainer_.pop_front();
89			} else if (indexContainer_.front().first < indexContainer_.front().second) {
90			++indexContainer_.front().first;
91			} else {
92			std::cerr << "" << std::endl;
93			}
94	gezelter	246
95	gezelter	507	return result;
96			}
97	gezelter	246
98
99	gezelter	507	/**
100			*
101			*/
102			void insert(int index) {
103			IndexListContainerIterator insertPos = internalInsert(index, index);
104			merge(insertPos);
105			}
106	gezelter	246
107	gezelter	507	/**
108			* Reclaims an index range
109			* @param beginIndex
110			* @param endIndex
111			*/
112			void insert(int beginIndex, int endIndex) {
113			IndexListContainerIterator insertPos = internalInsert(beginIndex, endIndex);
114			merge(insertPos);
115			}
116	gezelter	246
117	gezelter	507	/**
118			* Reclaims an index array.
119			* @param indices
120			*/
121			void insert(std::vector<int>& indices){
122	gezelter	246
123	gezelter	507	if (indices.empty()) {
124			return;
125			}
126	gezelter	246
127	gezelter	507	std::sort(indices.begin(), indices.end());
128			std::unique(indices.begin(), indices.end());
129	gezelter	246
130	gezelter	507	std::vector<int>::iterator i;
131			int beginIndex;
132	gezelter	246
133	gezelter	507	beginIndex = indices[0];
134	gezelter	246
135	gezelter	507	for ( i = indices.begin() + 1 ; i != indices.end(); ++i) {
136			if (i != (i -1) + 1) {
137			insert(beginIndex, *(i-1));
138			beginIndex = *i;
139			}
140			}
141			}
142	gezelter	246
143	gezelter	507	std::vector<int> getIndicesBefore(int index) {
144			std::vector<int> result;
145			IndexListContainerIterator i;
146	gezelter	246
147	gezelter	507	for(i = indexContainer_.begin(); i != indexContainer_.end(); ++i) {
148			if ((*i).first > index) {
149			//we locate the node whose minimum index is greater that index
150			indexContainer_.erase(indexContainer_.begin(), i);
151			break;
152			} else if ((*i).second < index) {
153			//The biggest index current node hold is less than the index we want
154			for (int j = (i).first; j <= (i).second; ++j) {
155			result.push_back(j);
156			}
157			continue;
158			} else if ((i).first == (i).second) {
159			//the index happen to equal to a node which only contains one index
160			result.push_back((*i).first);
161			indexContainer_.erase(indexContainer_.begin(), i);
162			break;
163			} else {
164	gezelter	246
165	gezelter	507	for (int j = (*i).first; j < index; ++j) {
166			result.push_back(j);
167			}
168	gezelter	246
169	gezelter	507	(*i).first = index;
170			indexContainer_.erase(indexContainer_.begin(), i);
171			break;
172			}
173	gezelter	246
174	gezelter	507	}
175	gezelter	246
176	gezelter	507	return result;
177	gezelter	246
178	gezelter	507	}
179	gezelter	246
180	gezelter	507	int getMaxIndex() {
181			return maxIndex_;
182			}
183	gezelter	246
184	gezelter	507	private:
185	gezelter	246
186	gezelter	507	IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {
187	gezelter	246
188	gezelter	507	if (beginIndex > endIndex) {
189			std::swap(beginIndex, endIndex);
190			std::cerr << "" << std::endl;
191			}
192	gezelter	246
193	gezelter	507	if (endIndex > maxIndex_) {
194			std::cerr << "" << std::endl;
195			}
196	gezelter	1874
197	gezelter	507	IndexListContainerIterator i = indexContainer_.begin();
198			for (; i != indexContainer_.end(); ++i) {
199			if ((*i).first > endIndex) {
200			indexContainer_.insert(i, std::make_pair(beginIndex, endIndex));
201			return --i;
202			} else if ((*i).second < beginIndex) {
203			continue;
204			} else {
205			std::cerr << "" << std::endl;
206			}
207			}
208	gezelter	246
209	gezelter	507	indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
210			return --indexContainer_.end();
211	gezelter	246
212	gezelter	507	}
213	gezelter	246
214	gezelter	507	void merge(IndexListContainerIterator i) {
215			IndexListContainerIterator j;
216	gezelter	246
217	gezelter	507	//check whether current node can be merged with its previous node
218			if ( i != indexContainer_.begin()) {
219			j = i;
220			--j;
221			if (j != indexContainer_.begin() && (j).second + 1 == (i).first) {
222			(i).first = (j).first;
223			indexContainer_.erase(j);
224			}
225			}
226	gezelter	246
227	gezelter	507	//check whether current node can be merged with its next node
228			if ( i != indexContainer_.end()) {
229			j = i;
230			++j;
231	gezelter	246
232	gezelter	507	if (j != indexContainer_.end() && (i).second + 1 == (j).first) {
233			(i).second = (j).second;
234			indexContainer_.erase(j);
235			}
236			}
237	gezelter	246
238	gezelter	507	}
239			int minIndex_;
240			int maxIndex_;
241			std::list<std::pair<int, int> > indexContainer_;
242			};
243	gezelter	246
244
245	gezelter	507	/**
246			* @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
247			* @brief
248			*/
249			class LocalIndexManager {
250			public:
251	gezelter	246
252	gezelter	507	int getNextAtomIndex() {
253			return atomIndexContainer_.pop();
254			}
255	gezelter	246
256	gezelter	507	std::vector<int> getAtomIndicesBefore(int index) {
257			return atomIndexContainer_.getIndicesBefore(index);
258			}
259	gezelter	246
260	gezelter	507	void releaseAtomIndex(int index) {
261			atomIndexContainer_.insert(index);
262			}
263	gezelter	246
264	gezelter	507	void releaseAtomIndex(int beginIndex, int endIndex) {
265			atomIndexContainer_.insert(beginIndex, endIndex);
266			}
267	gezelter	246
268	gezelter	507	void releaseAtomIndex(std::vector<int> indices) {
269			atomIndexContainer_.insert(indices);
270			}
271	gezelter	246
272	gezelter	507	int getNextRigidBodyIndex() {
273			return rigidBodyIndexContainer_.pop();
274			}
275	gezelter	246
276	gezelter	507	std::vector<int> getRigidBodyIndicesBefore(int index) {
277			return rigidBodyIndexContainer_.getIndicesBefore(index);
278			}
279	gezelter	246
280	gezelter	507	void releaseRigidBodyIndex(int index) {
281			rigidBodyIndexContainer_.insert(index);
282			}
283	gezelter	246
284	gezelter	507	void releaseRigidBodyIndex(int beginIndex, int endIndex) {
285			rigidBodyIndexContainer_.insert(beginIndex, endIndex);
286			}
287	gezelter	246
288	gezelter	507	void releaseRigidBodyIndex(std::vector<int> indices) {
289			rigidBodyIndexContainer_.insert(indices);
290			}
291	gezelter	1540
292			int getNextCutoffGroupIndex() {
293			return cutoffGroupIndexContainer_.pop();
294			}
295
296			std::vector<int> getCutoffGroupIndicesBefore(int index) {
297			return cutoffGroupIndexContainer_.getIndicesBefore(index);
298			}
299
300			void releaseCutoffGroupIndex(int index) {
301			cutoffGroupIndexContainer_.insert(index);
302			}
303
304			void releaseCutoffGroupIndex(int beginIndex, int endIndex) {
305			cutoffGroupIndexContainer_.insert(beginIndex, endIndex);
306			}
307
308			void releaseCutoffGroupIndex(std::vector<int> indices) {
309			cutoffGroupIndexContainer_.insert(indices);
310			}
311	gezelter	246
312	gezelter	507	private:
313	gezelter	246
314	gezelter	507	IndexListContainer atomIndexContainer_;
315			IndexListContainer rigidBodyIndexContainer_;
316	gezelter	1540	IndexListContainer cutoffGroupIndexContainer_;
317	gezelter	507	};
318	gezelter	246
319	gezelter	1390	} //end namespace OpenMD
320	gezelter	246	#endif //UTILS_LOCALINDEXMANAGER_HPP