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, 24107 (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;
      }

      IndexListContainerIterator i = indexContainer_.begin();
      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;
      IndexListContainerIterator insertPos;
      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 j;

      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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	9269 byte(s)
Log Message:	updated copyright notices
#	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			* [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	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	IndexListContainerIterator i = indexContainer_.begin();
84			int result;
85	gezelter	246
86	gezelter	507	result = indexContainer_.front().first;
87	gezelter	246
88	gezelter	507	if (indexContainer_.front().first == indexContainer_.front().second) {
89			indexContainer_.pop_front();
90			} else if (indexContainer_.front().first < indexContainer_.front().second) {
91			++indexContainer_.front().first;
92			} else {
93			std::cerr << "" << std::endl;
94			}
95	gezelter	246
96	gezelter	507	return result;
97			}
98	gezelter	246
99
100	gezelter	507	/**
101			*
102			*/
103			void insert(int index) {
104			IndexListContainerIterator insertPos = internalInsert(index, index);
105			merge(insertPos);
106			}
107	gezelter	246
108	gezelter	507	/**
109			* Reclaims an index range
110			* @param beginIndex
111			* @param endIndex
112			*/
113			void insert(int beginIndex, int endIndex) {
114			IndexListContainerIterator insertPos = internalInsert(beginIndex, endIndex);
115			merge(insertPos);
116			}
117	gezelter	246
118	gezelter	507	/**
119			* Reclaims an index array.
120			* @param indices
121			*/
122			void insert(std::vector<int>& indices){
123	gezelter	246
124	gezelter	507	if (indices.empty()) {
125			return;
126			}
127	gezelter	246
128	gezelter	507	std::sort(indices.begin(), indices.end());
129			std::unique(indices.begin(), indices.end());
130	gezelter	246
131	gezelter	507	std::vector<int>::iterator i;
132			IndexListContainerIterator insertPos;
133			int beginIndex;
134	gezelter	246
135	gezelter	507	beginIndex = indices[0];
136	gezelter	246
137	gezelter	507	for ( i = indices.begin() + 1 ; i != indices.end(); ++i) {
138			if (i != (i -1) + 1) {
139			insert(beginIndex, *(i-1));
140			beginIndex = *i;
141			}
142			}
143	gezelter	246
144
145	gezelter	507	}
146	gezelter	246
147	gezelter	507	std::vector<int> getIndicesBefore(int index) {
148			std::vector<int> result;
149			IndexListContainerIterator i;
150	gezelter	246
151	gezelter	507	for(i = indexContainer_.begin(); i != indexContainer_.end(); ++i) {
152			if ((*i).first > index) {
153			//we locate the node whose minimum index is greater that index
154			indexContainer_.erase(indexContainer_.begin(), i);
155			break;
156			} else if ((*i).second < index) {
157			//The biggest index current node hold is less than the index we want
158			for (int j = (i).first; j <= (i).second; ++j) {
159			result.push_back(j);
160			}
161			continue;
162			} else if ((i).first == (i).second) {
163			//the index happen to equal to a node which only contains one index
164			result.push_back((*i).first);
165			indexContainer_.erase(indexContainer_.begin(), i);
166			break;
167			} else {
168	gezelter	246
169	gezelter	507	for (int j = (*i).first; j < index; ++j) {
170			result.push_back(j);
171			}
172	gezelter	246
173	gezelter	507	(*i).first = index;
174			indexContainer_.erase(indexContainer_.begin(), i);
175			break;
176			}
177	gezelter	246
178	gezelter	507	}
179	gezelter	246
180	gezelter	507	return result;
181	gezelter	246
182	gezelter	507	}
183	gezelter	246
184	gezelter	507	int getMaxIndex() {
185			return maxIndex_;
186			}
187	gezelter	246
188	gezelter	507	private:
189	gezelter	246
190	gezelter	507	IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {
191	gezelter	246
192	gezelter	507	if (beginIndex > endIndex) {
193			std::swap(beginIndex, endIndex);
194			std::cerr << "" << std::endl;
195			}
196	gezelter	246
197	gezelter	507	if (endIndex > maxIndex_) {
198			std::cerr << "" << std::endl;
199			}
200	gezelter	246
201
202	gezelter	507	IndexListContainerIterator j;
203	gezelter	246
204	gezelter	507	IndexListContainerIterator i = indexContainer_.begin();
205			for (; i != indexContainer_.end(); ++i) {
206			if ((*i).first > endIndex) {
207			indexContainer_.insert(i, std::make_pair(beginIndex, endIndex));
208			return --i;
209			} else if ((*i).second < beginIndex) {
210			continue;
211			} else {
212			std::cerr << "" << std::endl;
213			}
214			}
215	gezelter	246
216	gezelter	507	indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
217			return --indexContainer_.end();
218	gezelter	246
219	gezelter	507	}
220	gezelter	246
221	gezelter	507	void merge(IndexListContainerIterator i) {
222			IndexListContainerIterator j;
223	gezelter	246
224	gezelter	507	//check whether current node can be merged with its previous node
225			if ( i != indexContainer_.begin()) {
226			j = i;
227			--j;
228			if (j != indexContainer_.begin() && (j).second + 1 == (i).first) {
229			(i).first = (j).first;
230			indexContainer_.erase(j);
231			}
232			}
233	gezelter	246
234	gezelter	507	//check whether current node can be merged with its next node
235			if ( i != indexContainer_.end()) {
236			j = i;
237			++j;
238	gezelter	246
239	gezelter	507	if (j != indexContainer_.end() && (i).second + 1 == (j).first) {
240			(i).second = (j).second;
241			indexContainer_.erase(j);
242			}
243			}
244	gezelter	246
245	gezelter	507	}
246			int minIndex_;
247			int maxIndex_;
248			std::list<std::pair<int, int> > indexContainer_;
249			};
250	gezelter	246
251
252	gezelter	507	/**
253			* @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
254			* @brief
255			*/
256			class LocalIndexManager {
257			public:
258	gezelter	246
259	gezelter	507	int getNextAtomIndex() {
260			return atomIndexContainer_.pop();
261			}
262	gezelter	246
263	gezelter	507	std::vector<int> getAtomIndicesBefore(int index) {
264			return atomIndexContainer_.getIndicesBefore(index);
265			}
266	gezelter	246
267	gezelter	507	void releaseAtomIndex(int index) {
268			atomIndexContainer_.insert(index);
269			}
270	gezelter	246
271	gezelter	507	void releaseAtomIndex(int beginIndex, int endIndex) {
272			atomIndexContainer_.insert(beginIndex, endIndex);
273			}
274	gezelter	246
275	gezelter	507	void releaseAtomIndex(std::vector<int> indices) {
276			atomIndexContainer_.insert(indices);
277			}
278	gezelter	246
279	gezelter	507	int getNextRigidBodyIndex() {
280			return rigidBodyIndexContainer_.pop();
281			}
282	gezelter	246
283	gezelter	507	std::vector<int> getRigidBodyIndicesBefore(int index) {
284			return rigidBodyIndexContainer_.getIndicesBefore(index);
285			}
286	gezelter	246
287	gezelter	507	void releaseRigidBodyIndex(int index) {
288			rigidBodyIndexContainer_.insert(index);
289			}
290	gezelter	246
291	gezelter	507	void releaseRigidBodyIndex(int beginIndex, int endIndex) {
292			rigidBodyIndexContainer_.insert(beginIndex, endIndex);
293			}
294	gezelter	246
295	gezelter	507	void releaseRigidBodyIndex(std::vector<int> indices) {
296			rigidBodyIndexContainer_.insert(indices);
297			}
298	gezelter	1540
299			int getNextCutoffGroupIndex() {
300			return cutoffGroupIndexContainer_.pop();
301			}
302
303			std::vector<int> getCutoffGroupIndicesBefore(int index) {
304			return cutoffGroupIndexContainer_.getIndicesBefore(index);
305			}
306
307			void releaseCutoffGroupIndex(int index) {
308			cutoffGroupIndexContainer_.insert(index);
309			}
310
311			void releaseCutoffGroupIndex(int beginIndex, int endIndex) {
312			cutoffGroupIndexContainer_.insert(beginIndex, endIndex);
313			}
314
315			void releaseCutoffGroupIndex(std::vector<int> indices) {
316			cutoffGroupIndexContainer_.insert(indices);
317			}
318	gezelter	246
319	gezelter	507	private:
320	gezelter	246
321	gezelter	507	IndexListContainer atomIndexContainer_;
322			IndexListContainer rigidBodyIndexContainer_;
323	gezelter	1540	IndexListContainer cutoffGroupIndexContainer_;
324	gezelter	507	};
325	gezelter	246
326	gezelter	1390	} //end namespace OpenMD
327	gezelter	246	#endif //UTILS_LOCALINDEXMANAGER_HPP