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);
    }
    
    int getNextBondIndex() {
      return bondIndexContainer_.pop();
    }

    std::vector<int> getBondIndicesBefore(int index) {
      return bondIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseBondIndex(int index) {
      bondIndexContainer_.insert(index);
    }

    void releaseBondIndex(int beginIndex, int endIndex) {
      bondIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseBondIndex(std::vector<int> indices) {
      bondIndexContainer_.insert(indices);
    }

    int getNextBendIndex() {
      return bendIndexContainer_.pop();
    }

    std::vector<int> getBendIndicesBefore(int index) {
      return bendIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseBendIndex(int index) {
      bendIndexContainer_.insert(index);
    }

    void releaseBendIndex(int beginIndex, int endIndex) {
      bendIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseBendIndex(std::vector<int> indices) {
      bendIndexContainer_.insert(indices);
    }

    int getNextTorsionIndex() {
      return torsionIndexContainer_.pop();
    }

    std::vector<int> getTorsionIndicesBefore(int index) {
      return torsionIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseTorsionIndex(int index) {
      torsionIndexContainer_.insert(index);
    }

    void releaseTorsionIndex(int beginIndex, int endIndex) {
      torsionIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseTorsionIndex(std::vector<int> indices) {
      torsionIndexContainer_.insert(indices);
    }

    int getNextInversionIndex() {
      return inversionIndexContainer_.pop();
    }

    std::vector<int> getInversionIndicesBefore(int index) {
      return inversionIndexContainer_.getIndicesBefore(index);
    }
        
    void releaseInversionIndex(int index) {
      inversionIndexContainer_.insert(index);
    }

    void releaseInversionIndex(int beginIndex, int endIndex) {
      inversionIndexContainer_.insert(beginIndex, endIndex);
    }

    void releaseInversionIndex(std::vector<int> indices) {
      inversionIndexContainer_.insert(indices);
    }

  private:

    IndexListContainer atomIndexContainer_;
    IndexListContainer rigidBodyIndexContainer_;
    IndexListContainer cutoffGroupIndexContainer_;
    IndexListContainer bondIndexContainer_;
    IndexListContainer bendIndexContainer_;
    IndexListContainer torsionIndexContainer_;
    IndexListContainer inversionIndexContainer_;
  };

} //end namespace OpenMD
#endif //UTILS_LOCALINDEXMANAGER_HPP
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	11446 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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, 234107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	namespace OpenMD {
59
60	/**
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
70	IndexListContainer(int minIndex = 0, int maxIndex = MAX_INTEGER)
71	:minIndex_(minIndex), maxIndex_(maxIndex) {
72	indexContainer_.push_back(std::make_pair(minIndex, maxIndex));
73	}
74
75	int pop() {
76	if (indexContainer_.empty()) {
77	std::cerr << "" << std::endl;
78	}
79
80	int result;
81
82	result = indexContainer_.front().first;
83
84	if (indexContainer_.front().first == indexContainer_.front().second) {
85	indexContainer_.pop_front();
86	} else if (indexContainer_.front().first <
87	indexContainer_.front().second) {
88	++indexContainer_.front().first;
89	} else {
90	std::cerr << "" << std::endl;
91	}
92
93	return result;
94	}
95
96
97	/**
98	*
99	*/
100	void insert(int index) {
101	IndexListContainerIterator insertPos = internalInsert(index, index);
102	merge(insertPos);
103	}
104
105	/**
106	* Reclaims an index range
107	* @param beginIndex
108	* @param endIndex
109	*/
110	void insert(int beginIndex, int endIndex) {
111	IndexListContainerIterator insertPos = internalInsert(beginIndex,
112	endIndex);
113	merge(insertPos);
114	}
115
116	/**
117	* Reclaims an index array.
118	* @param indices
119	*/
120	void insert(std::vector<int>& indices){
121
122	if (indices.empty()) {
123	return;
124	}
125
126	std::sort(indices.begin(), indices.end());
127	std::unique(indices.begin(), indices.end());
128
129	std::vector<int>::iterator i;
130	int beginIndex;
131
132	beginIndex = indices[0];
133
134	for ( i = indices.begin() + 1 ; i != indices.end(); ++i) {
135	if (i != (i -1) + 1) {
136	insert(beginIndex, *(i-1));
137	beginIndex = *i;
138	}
139	}
140	}
141
142	std::vector<int> getIndicesBefore(int index) {
143	std::vector<int> result;
144	IndexListContainerIterator i;
145
146	for(i = indexContainer_.begin(); i != indexContainer_.end(); ++i) {
147	if ((*i).first > index) {
148	//we locate the node whose minimum index is greater that index
149	indexContainer_.erase(indexContainer_.begin(), i);
150	break;
151	} else if ((*i).second < index) {
152	//The biggest index current node hold is less than the index we want
153	for (int j = (i).first; j <= (i).second; ++j) {
154	result.push_back(j);
155	}
156	continue;
157	} else if ((i).first == (i).second) {
158	//the index happen to equal to a node which only contains one index
159	result.push_back((*i).first);
160	indexContainer_.erase(indexContainer_.begin(), i);
161	break;
162	} else {
163	for (int j = (*i).first; j < index; ++j) {
164	result.push_back(j);
165	}
166	(*i).first = index;
167	indexContainer_.erase(indexContainer_.begin(), i);
168	break;
169	}
170	}
171	return result;
172	}
173
174	int getMaxIndex() {
175	return maxIndex_;
176	}
177
178	private:
179
180	IndexListContainerIterator internalInsert(int beginIndex, int endIndex) {
181
182	if (beginIndex > endIndex) {
183	std::swap(beginIndex, endIndex);
184	std::cerr << "" << std::endl;
185	}
186
187	if (endIndex > maxIndex_) {
188	std::cerr << "" << std::endl;
189	}
190
191	IndexListContainerIterator i = indexContainer_.begin();
192	for (; i != indexContainer_.end(); ++i) {
193	if ((*i).first > endIndex) {
194	indexContainer_.insert(i, std::make_pair(beginIndex, endIndex));
195	return --i;
196	} else if ((*i).second < beginIndex) {
197	continue;
198	} else {
199	std::cerr << "" << std::endl;
200	}
201	}
202
203	indexContainer_.push_back(std::make_pair(beginIndex, endIndex));
204	return --indexContainer_.end();
205
206	}
207
208	void merge(IndexListContainerIterator i) {
209	IndexListContainerIterator j;
210
211	//check whether current node can be merged with its previous node
212	if ( i != indexContainer_.begin()) {
213	j = i;
214	--j;
215	if (j != indexContainer_.begin() && (j).second + 1 == (i).first) {
216	(i).first = (j).first;
217	indexContainer_.erase(j);
218	}
219	}
220
221	//check whether current node can be merged with its next node
222	if ( i != indexContainer_.end()) {
223	j = i;
224	++j;
225
226	if (j != indexContainer_.end() && (i).second + 1 == (j).first) {
227	(i).second = (j).second;
228	indexContainer_.erase(j);
229	}
230	}
231
232	}
233	int minIndex_;
234	int maxIndex_;
235	std::list<std::pair<int, int> > indexContainer_;
236	};
237
238
239	/**
240	* @class LocalIndexManager LocalIndexManager.hpp "utils/LocalIndexManager.hpp"
241	* @brief
242	*/
243	class LocalIndexManager {
244	public:
245
246	int getNextAtomIndex() {
247	return atomIndexContainer_.pop();
248	}
249
250	std::vector<int> getAtomIndicesBefore(int index) {
251	return atomIndexContainer_.getIndicesBefore(index);
252	}
253
254	void releaseAtomIndex(int index) {
255	atomIndexContainer_.insert(index);
256	}
257
258	void releaseAtomIndex(int beginIndex, int endIndex) {
259	atomIndexContainer_.insert(beginIndex, endIndex);
260	}
261
262	void releaseAtomIndex(std::vector<int> indices) {
263	atomIndexContainer_.insert(indices);
264	}
265
266	int getNextRigidBodyIndex() {
267	return rigidBodyIndexContainer_.pop();
268	}
269
270	std::vector<int> getRigidBodyIndicesBefore(int index) {
271	return rigidBodyIndexContainer_.getIndicesBefore(index);
272	}
273
274	void releaseRigidBodyIndex(int index) {
275	rigidBodyIndexContainer_.insert(index);
276	}
277
278	void releaseRigidBodyIndex(int beginIndex, int endIndex) {
279	rigidBodyIndexContainer_.insert(beginIndex, endIndex);
280	}
281
282	void releaseRigidBodyIndex(std::vector<int> indices) {
283	rigidBodyIndexContainer_.insert(indices);
284	}
285
286	int getNextCutoffGroupIndex() {
287	return cutoffGroupIndexContainer_.pop();
288	}
289
290	std::vector<int> getCutoffGroupIndicesBefore(int index) {
291	return cutoffGroupIndexContainer_.getIndicesBefore(index);
292	}
293
294	void releaseCutoffGroupIndex(int index) {
295	cutoffGroupIndexContainer_.insert(index);
296	}
297
298	void releaseCutoffGroupIndex(int beginIndex, int endIndex) {
299	cutoffGroupIndexContainer_.insert(beginIndex, endIndex);
300	}
301
302	void releaseCutoffGroupIndex(std::vector<int> indices) {
303	cutoffGroupIndexContainer_.insert(indices);
304	}
305
306	int getNextBondIndex() {
307	return bondIndexContainer_.pop();
308	}
309
310	std::vector<int> getBondIndicesBefore(int index) {
311	return bondIndexContainer_.getIndicesBefore(index);
312	}
313
314	void releaseBondIndex(int index) {
315	bondIndexContainer_.insert(index);
316	}
317
318	void releaseBondIndex(int beginIndex, int endIndex) {
319	bondIndexContainer_.insert(beginIndex, endIndex);
320	}
321
322	void releaseBondIndex(std::vector<int> indices) {
323	bondIndexContainer_.insert(indices);
324	}
325
326	int getNextBendIndex() {
327	return bendIndexContainer_.pop();
328	}
329
330	std::vector<int> getBendIndicesBefore(int index) {
331	return bendIndexContainer_.getIndicesBefore(index);
332	}
333
334	void releaseBendIndex(int index) {
335	bendIndexContainer_.insert(index);
336	}
337
338	void releaseBendIndex(int beginIndex, int endIndex) {
339	bendIndexContainer_.insert(beginIndex, endIndex);
340	}
341
342	void releaseBendIndex(std::vector<int> indices) {
343	bendIndexContainer_.insert(indices);
344	}
345
346	int getNextTorsionIndex() {
347	return torsionIndexContainer_.pop();
348	}
349
350	std::vector<int> getTorsionIndicesBefore(int index) {
351	return torsionIndexContainer_.getIndicesBefore(index);
352	}
353
354	void releaseTorsionIndex(int index) {
355	torsionIndexContainer_.insert(index);
356	}
357
358	void releaseTorsionIndex(int beginIndex, int endIndex) {
359	torsionIndexContainer_.insert(beginIndex, endIndex);
360	}
361
362	void releaseTorsionIndex(std::vector<int> indices) {
363	torsionIndexContainer_.insert(indices);
364	}
365
366	int getNextInversionIndex() {
367	return inversionIndexContainer_.pop();
368	}
369
370	std::vector<int> getInversionIndicesBefore(int index) {
371	return inversionIndexContainer_.getIndicesBefore(index);
372	}
373
374	void releaseInversionIndex(int index) {
375	inversionIndexContainer_.insert(index);
376	}
377
378	void releaseInversionIndex(int beginIndex, int endIndex) {
379	inversionIndexContainer_.insert(beginIndex, endIndex);
380	}
381
382	void releaseInversionIndex(std::vector<int> indices) {
383	inversionIndexContainer_.insert(indices);
384	}
385
386	private:
387
388	IndexListContainer atomIndexContainer_;
389	IndexListContainer rigidBodyIndexContainer_;
390	IndexListContainer cutoffGroupIndexContainer_;
391	IndexListContainer bondIndexContainer_;
392	IndexListContainer bendIndexContainer_;
393	IndexListContainer torsionIndexContainer_;
394	IndexListContainer inversionIndexContainer_;
395	};
396
397	} //end namespace OpenMD
398	#endif //UTILS_LOCALINDEXMANAGER_HPP