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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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);
    }
 
  private:

    IndexListContainer atomIndexContainer_;
    IndexListContainer rigidBodyIndexContainer_;
  };

} //end namespace OpenMD
#endif //UTILS_LOCALINDEXMANAGER_HPP
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	8566 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			/**
43			* @file LocalIndexManager.hpp
44			* @author tlin
45			* @date 11/02/2004
46			* @version 1.0
47			*/
48
49			#ifndef UTILS_LOCALINDEXMANAGER_HPP
50			#define UTILS_LOCALINDEXMANAGER_HPP
51			#include <algorithm>
52			#include <iostream>
53			#include <cassert>
54			#include <list>
55			#include <utility>
56
57	gezelter	1390	namespace OpenMD {
58	gezelter	246
59	gezelter	507	/**
60			* @class IndexListContainer
61			* @brief
62			* @todo documentation
63			*/
64			class IndexListContainer{
65			public:
66			static const int MAX_INTEGER = 2147483647;
67			typedef std::list<std::pair<int, int> >::iterator IndexListContainerIterator;
68	gezelter	246
69
70	gezelter	507	IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER)
71			:minIndex_(minIndex), maxIndex_(maxIndex) {
72	gezelter	246
73	gezelter	507	indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
74			}
75	gezelter	246
76	gezelter	507	int pop() {
77	gezelter	246
78	gezelter	507	if (indexContainer_.empty()) {
79			std::cerr << "" << std::endl;
80			}
81	gezelter	246
82	gezelter	507	IndexListContainerIterator i = indexContainer_.begin();
83			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			IndexListContainerIterator insertPos;
132			int beginIndex;
133	gezelter	246
134	gezelter	507	beginIndex = indices[0];
135	gezelter	246
136	gezelter	507	for ( i = indices.begin() + 1 ; i != indices.end(); ++i) {
137			if (i != (i -1) + 1) {
138			insert(beginIndex, *(i-1));
139			beginIndex = *i;
140			}
141			}
142	gezelter	246
143
144	gezelter	507	}
145	gezelter	246
146	gezelter	507	std::vector<int> getIndicesBefore(int index) {
147			std::vector<int> result;
148			IndexListContainerIterator i;
149	gezelter	246
150	gezelter	507	for(i = indexContainer_.begin(); i != indexContainer_.end(); ++i) {
151			if ((*i).first > index) {
152			//we locate the node whose minimum index is greater that index
153			indexContainer_.erase(indexContainer_.begin(), i);
154			break;
155			} else if ((*i).second < index) {
156			//The biggest index current node hold is less than the index we want
157			for (int j = (i).first; j <= (i).second; ++j) {
158			result.push_back(j);
159			}
160			continue;
161			} else if ((i).first == (i).second) {
162			//the index happen to equal to a node which only contains one index
163			result.push_back((*i).first);
164			indexContainer_.erase(indexContainer_.begin(), i);
165			break;
166			} else {
167	gezelter	246
168	gezelter	507	for (int j = (*i).first; j < index; ++j) {
169			result.push_back(j);
170			}
171	gezelter	246
172	gezelter	507	(*i).first = index;
173			indexContainer_.erase(indexContainer_.begin(), i);
174			break;
175			}
176	gezelter	246
177	gezelter	507	}
178	gezelter	246
179	gezelter	507	return result;
180	gezelter	246
181	gezelter	507	}
182	gezelter	246
183	gezelter	507	int getMaxIndex() {
184			return maxIndex_;
185			}
186	gezelter	246
187	gezelter	507	private:
188	gezelter	246
189	gezelter	507	IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {
190	gezelter	246
191	gezelter	507	if (beginIndex > endIndex) {
192			std::swap(beginIndex, endIndex);
193			std::cerr << "" << std::endl;
194			}
195	gezelter	246
196	gezelter	507	if (endIndex > maxIndex_) {
197			std::cerr << "" << std::endl;
198			}
199	gezelter	246
200
201	gezelter	507	IndexListContainerIterator j;
202	gezelter	246
203	gezelter	507	IndexListContainerIterator i = indexContainer_.begin();
204			for (; i != indexContainer_.end(); ++i) {
205			if ((*i).first > endIndex) {
206			indexContainer_.insert(i, std::make_pair(beginIndex, endIndex));
207			return --i;
208			} else if ((*i).second < beginIndex) {
209			continue;
210			} else {
211			std::cerr << "" << std::endl;
212			}
213			}
214	gezelter	246
215	gezelter	507	indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
216			return --indexContainer_.end();
217	gezelter	246
218	gezelter	507	}
219	gezelter	246
220	gezelter	507	void merge(IndexListContainerIterator i) {
221			IndexListContainerIterator j;
222	gezelter	246
223	gezelter	507	//check whether current node can be merged with its previous node
224			if ( i != indexContainer_.begin()) {
225			j = i;
226			--j;
227			if (j != indexContainer_.begin() && (j).second + 1 == (i).first) {
228			(i).first = (j).first;
229			indexContainer_.erase(j);
230			}
231			}
232	gezelter	246
233	gezelter	507	//check whether current node can be merged with its next node
234			if ( i != indexContainer_.end()) {
235			j = i;
236			++j;
237	gezelter	246
238	gezelter	507	if (j != indexContainer_.end() && (i).second + 1 == (j).first) {
239			(i).second = (j).second;
240			indexContainer_.erase(j);
241			}
242			}
243	gezelter	246
244	gezelter	507	}
245			int minIndex_;
246			int maxIndex_;
247			std::list<std::pair<int, int> > indexContainer_;
248			};
249	gezelter	246
250
251	gezelter	507	/**
252			* @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
253			* @brief
254			*/
255			class LocalIndexManager {
256			public:
257	gezelter	246
258	gezelter	507	int getNextAtomIndex() {
259			return atomIndexContainer_.pop();
260			}
261	gezelter	246
262	gezelter	507	std::vector<int> getAtomIndicesBefore(int index) {
263			return atomIndexContainer_.getIndicesBefore(index);
264			}
265	gezelter	246
266	gezelter	507	void releaseAtomIndex(int index) {
267			atomIndexContainer_.insert(index);
268			}
269	gezelter	246
270	gezelter	507	void releaseAtomIndex(int beginIndex, int endIndex) {
271			atomIndexContainer_.insert(beginIndex, endIndex);
272			}
273	gezelter	246
274	gezelter	507	void releaseAtomIndex(std::vector<int> indices) {
275			atomIndexContainer_.insert(indices);
276			}
277	gezelter	246
278	gezelter	507	int getNextRigidBodyIndex() {
279			return rigidBodyIndexContainer_.pop();
280			}
281	gezelter	246
282	gezelter	507	std::vector<int> getRigidBodyIndicesBefore(int index) {
283			return rigidBodyIndexContainer_.getIndicesBefore(index);
284			}
285	gezelter	246
286	gezelter	507	void releaseRigidBodyIndex(int index) {
287			rigidBodyIndexContainer_.insert(index);
288			}
289	gezelter	246
290	gezelter	507	void releaseRigidBodyIndex(int beginIndex, int endIndex) {
291			rigidBodyIndexContainer_.insert(beginIndex, endIndex);
292			}
293	gezelter	246
294	gezelter	507	void releaseRigidBodyIndex(std::vector<int> indices) {
295			rigidBodyIndexContainer_.insert(indices);
296			}
297	gezelter	246
298	gezelter	507	private:
299	gezelter	246
300	gezelter	507	IndexListContainer atomIndexContainer_;
301			IndexListContainer rigidBodyIndexContainer_;
302			};
303	gezelter	246
304	gezelter	1390	} //end namespace OpenMD
305	gezelter	246	#endif //UTILS_LOCALINDEXMANAGER_HPP