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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (15 years, 3 months ago) by chuckv
File size:	8566 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
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	namespace OpenMD {
58
59	/**
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
69
70	IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER)
71	:minIndex_(minIndex), maxIndex_(maxIndex) {
72
73	indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
74	}
75
76	int pop() {
77
78	if (indexContainer_.empty()) {
79	std::cerr << "" << std::endl;
80	}
81
82	IndexListContainerIterator i = indexContainer_.begin();
83	int result;
84
85	result = indexContainer_.front().first;
86
87	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
95	return result;
96	}
97
98
99	/**
100	*
101	*/
102	void insert(int index) {
103	IndexListContainerIterator insertPos = internalInsert(index, index);
104	merge(insertPos);
105	}
106
107	/**
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
117	/**
118	* Reclaims an index array.
119	* @param indices
120	*/
121	void insert(std::vector<int>& indices){
122
123	if (indices.empty()) {
124	return;
125	}
126
127	std::sort(indices.begin(), indices.end());
128	std::unique(indices.begin(), indices.end());
129
130	std::vector<int>::iterator i;
131	IndexListContainerIterator insertPos;
132	int beginIndex;
133
134	beginIndex = indices[0];
135
136	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
143
144	}
145
146	std::vector<int> getIndicesBefore(int index) {
147	std::vector<int> result;
148	IndexListContainerIterator i;
149
150	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
168	for (int j = (*i).first; j < index; ++j) {
169	result.push_back(j);
170	}
171
172	(*i).first = index;
173	indexContainer_.erase(indexContainer_.begin(), i);
174	break;
175	}
176
177	}
178
179	return result;
180
181	}
182
183	int getMaxIndex() {
184	return maxIndex_;
185	}
186
187	private:
188
189	IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {
190
191	if (beginIndex > endIndex) {
192	std::swap(beginIndex, endIndex);
193	std::cerr << "" << std::endl;
194	}
195
196	if (endIndex > maxIndex_) {
197	std::cerr << "" << std::endl;
198	}
199
200
201	IndexListContainerIterator j;
202
203	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
215	indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
216	return --indexContainer_.end();
217
218	}
219
220	void merge(IndexListContainerIterator i) {
221	IndexListContainerIterator j;
222
223	//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
233	//check whether current node can be merged with its next node
234	if ( i != indexContainer_.end()) {
235	j = i;
236	++j;
237
238	if (j != indexContainer_.end() && (i).second + 1 == (j).first) {
239	(i).second = (j).second;
240	indexContainer_.erase(j);
241	}
242	}
243
244	}
245	int minIndex_;
246	int maxIndex_;
247	std::list<std::pair<int, int> > indexContainer_;
248	};
249
250
251	/**
252	* @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
253	* @brief
254	*/
255	class LocalIndexManager {
256	public:
257
258	int getNextAtomIndex() {
259	return atomIndexContainer_.pop();
260	}
261
262	std::vector<int> getAtomIndicesBefore(int index) {
263	return atomIndexContainer_.getIndicesBefore(index);
264	}
265
266	void releaseAtomIndex(int index) {
267	atomIndexContainer_.insert(index);
268	}
269
270	void releaseAtomIndex(int beginIndex, int endIndex) {
271	atomIndexContainer_.insert(beginIndex, endIndex);
272	}
273
274	void releaseAtomIndex(std::vector<int> indices) {
275	atomIndexContainer_.insert(indices);
276	}
277
278	int getNextRigidBodyIndex() {
279	return rigidBodyIndexContainer_.pop();
280	}
281
282	std::vector<int> getRigidBodyIndicesBefore(int index) {
283	return rigidBodyIndexContainer_.getIndicesBefore(index);
284	}
285
286	void releaseRigidBodyIndex(int index) {
287	rigidBodyIndexContainer_.insert(index);
288	}
289
290	void releaseRigidBodyIndex(int beginIndex, int endIndex) {
291	rigidBodyIndexContainer_.insert(beginIndex, endIndex);
292	}
293
294	void releaseRigidBodyIndex(std::vector<int> indices) {
295	rigidBodyIndexContainer_.insert(indices);
296	}
297
298	private:
299
300	IndexListContainer atomIndexContainer_;
301	IndexListContainer rigidBodyIndexContainer_;
302	};
303
304	} //end namespace OpenMD
305	#endif //UTILS_LOCALINDEXMANAGER_HPP