src/selection/SelectionSet.cpp

/*
 * 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).
 */

#ifdef IS_MPI
#include <mpi.h>
#endif

#include <algorithm>
#include <cassert>
#include <string>
#include <iterator>

#include "selection/SelectionSet.hpp"
#include "utils/Algorithm.hpp"

namespace OpenMD {

  SelectionSet::SelectionSet(std::vector<int> nbits) {
    bitsets_.resize(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++)
      bitsets_[i] = OpenMDBitSet(nbits[i]);
    clearAll();        
  }
  
  std::vector<int> SelectionSet::countBits() {
    std::vector<int> result(N_SELECTIONTYPES, 0);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].countBits();   
    return result;
  }

  void SelectionSet::flip(std::vector<int> bitIndex) { 
    for (int i = 0; i < N_SELECTIONTYPES; i++)
      bitsets_[i].flip(bitIndex[i]);
  }

  void SelectionSet::flip(std::vector<int> fromIndex, 
                          std::vector<int> toIndex) {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i].flip(fromIndex[i], toIndex[i]);
  }
  
  void SelectionSet::flip() {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i].flip();
  }

  std::vector<bool> SelectionSet::get(std::vector<int> bitIndex) {  
    std::vector<bool> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].get(bitIndex[i]);
    return result;
  }

  SelectionSet SelectionSet::get(std::vector<int> fromIndex, 
                                 std::vector<int> toIndex) {
    SelectionSet result;

    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result.bitsets_[i] = bitsets_[i].get(fromIndex[i], toIndex[i]);
    
    return result;
  }

  std::vector<bool> SelectionSet::any() {
    std::vector<bool> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++)       
      result[i] = bitsets_[i].any();
    return result;
  }

  std::vector<bool> SelectionSet::none() {
    std::vector<bool> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].none();
    return result;
  }

  std::vector<int> SelectionSet::firstOffBit() const {
    std::vector<int> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].firstOffBit();
    return result;
  }
  
  std::vector<int> SelectionSet::nextOffBit(std::vector<int> fromIndex) const {
    std::vector<int> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].nextOffBit(fromIndex[i]);
    return result;
  }

  std::vector<int> SelectionSet::firstOnBit() const {
    std::vector<int> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].firstOnBit();
    return result;
  }

  std::vector<int> SelectionSet::nextOnBit(std::vector<int> fromIndex) const {
    std::vector<int> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].nextOnBit(fromIndex[i]);
    return result;
  }

  void SelectionSet::andOperator (const SelectionSet& ss) {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i] &= ss.bitsets_[i];
  }

  void SelectionSet::orOperator (const SelectionSet& ss) {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i] |= ss.bitsets_[i];
  }

  void SelectionSet::xorOperator (const SelectionSet& ss) {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i] ^= ss.bitsets_[i];
  }
   
  //void SelectionSet::setBits(std::vector<int> fromIndex, 
  //                           std::vector<int> toIndex, bool value) {
  //  for (int i = 0; i < N_SELECTIONTYPES; i++) 
  //    bitsets_[i].setBits(fromIndex[i], toIndex[i], value);
  //}

  void SelectionSet::clearAll() {  
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i].clearAll();  
  }         

  void SelectionSet::setAll() {  
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i].setAll();  
  }

  std::vector<int> SelectionSet::size() const {  
    std::vector<int> result(N_SELECTIONTYPES);
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      result[i] = bitsets_[i].size();   
    return result;
  }
  
  void SelectionSet::resize(std::vector<int> nbits) {
    for (int i = 0; i < N_SELECTIONTYPES; i++) 
      bitsets_[i].resize(nbits[i]);   
  }

  SelectionSet operator| (const SelectionSet& ss1, const SelectionSet& ss2) {
    SelectionSet result(ss1);
    for (int i = 0; i < N_SELECTIONTYPES; i++)           
      result.bitsets_[i] |= ss2.bitsets_[i];
    return result;
  }

  SelectionSet operator& (const SelectionSet& ss1, const SelectionSet& ss2) {
    SelectionSet result(ss1);
    for (int i = 0; i < N_SELECTIONTYPES; i++)           
      result.bitsets_[i] &= ss2.bitsets_[i];
    return result;
  }

  SelectionSet operator^ (const SelectionSet& ss1, const SelectionSet& ss2) {
    SelectionSet result(ss1);
    for (int i = 0; i < N_SELECTIONTYPES; i++)           
      result.bitsets_[i] ^= ss2.bitsets_[i];
    return result;
  }

  SelectionSet operator- (const SelectionSet& ss1, const SelectionSet& ss2) {
    SelectionSet result(ss1);
    for (int i = 0; i < N_SELECTIONTYPES; i++)           
      result.bitsets_[i] -= ss2.bitsets_[i];
    return result;
  }

  bool operator== (const SelectionSet & ss1, const SelectionSet &ss2) {

    for (int i = 0; i < N_SELECTIONTYPES; i++) {
      assert(ss1.bitsets_[i].size() == ss2.bitsets_[i].size());      
      if (!(ss1.bitsets_[i] == ss2.bitsets_[i])) return false;
    }
      
    return true;
  }  

  SelectionSet SelectionSet::parallelReduce() {

    SelectionSet result;
    for (int i = 0; i < N_SELECTIONTYPES; i++)
      result.bitsets_[i] = bitsets_[i].parallelReduce();
    
    return result;
  }


  //std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
  //
  //    return is;
  //}

  std::ostream& operator<< ( std::ostream& os, const SelectionSet& ss) {
    for (int i = 0; i < N_SELECTIONTYPES; i++)
      os << "SelectionSet[" << i << "] = " << ss.bitsets_[i] << std::endl;
    return os;
  }

  //void SelectionSet::setBit(std::vector<int> bitIndex, bool value) { 
  //  for (int i = 0; i < N_SELECTIONTYPES; i++)      
  //    bitsets_[i].setBit(bitIndex[i], value);
  //}
          
}
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	8438 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	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include <algorithm>
48	#include <cassert>
49	#include <string>
50	#include <iterator>
51
52	#include "selection/SelectionSet.hpp"
53	#include "utils/Algorithm.hpp"
54
55	namespace OpenMD {
56
57	SelectionSet::SelectionSet(std::vector<int> nbits) {
58	bitsets_.resize(N_SELECTIONTYPES);
59	for (int i = 0; i < N_SELECTIONTYPES; i++)
60	bitsets_[i] = OpenMDBitSet(nbits[i]);
61	clearAll();
62	}
63
64	std::vector<int> SelectionSet::countBits() {
65	std::vector<int> result(N_SELECTIONTYPES, 0);
66	for (int i = 0; i < N_SELECTIONTYPES; i++)
67	result[i] = bitsets_[i].countBits();
68	return result;
69	}
70
71	void SelectionSet::flip(std::vector<int> bitIndex) {
72	for (int i = 0; i < N_SELECTIONTYPES; i++)
73	bitsets_[i].flip(bitIndex[i]);
74	}
75
76	void SelectionSet::flip(std::vector<int> fromIndex,
77	std::vector<int> toIndex) {
78	for (int i = 0; i < N_SELECTIONTYPES; i++)
79	bitsets_[i].flip(fromIndex[i], toIndex[i]);
80	}
81
82	void SelectionSet::flip() {
83	for (int i = 0; i < N_SELECTIONTYPES; i++)
84	bitsets_[i].flip();
85	}
86
87	std::vector<bool> SelectionSet::get(std::vector<int> bitIndex) {
88	std::vector<bool> result(N_SELECTIONTYPES);
89	for (int i = 0; i < N_SELECTIONTYPES; i++)
90	result[i] = bitsets_[i].get(bitIndex[i]);
91	return result;
92	}
93
94	SelectionSet SelectionSet::get(std::vector<int> fromIndex,
95	std::vector<int> toIndex) {
96	SelectionSet result;
97
98	for (int i = 0; i < N_SELECTIONTYPES; i++)
99	result.bitsets_[i] = bitsets_[i].get(fromIndex[i], toIndex[i]);
100
101	return result;
102	}
103
104	std::vector<bool> SelectionSet::any() {
105	std::vector<bool> result(N_SELECTIONTYPES);
106	for (int i = 0; i < N_SELECTIONTYPES; i++)
107	result[i] = bitsets_[i].any();
108	return result;
109	}
110
111	std::vector<bool> SelectionSet::none() {
112	std::vector<bool> result(N_SELECTIONTYPES);
113	for (int i = 0; i < N_SELECTIONTYPES; i++)
114	result[i] = bitsets_[i].none();
115	return result;
116	}
117
118	std::vector<int> SelectionSet::firstOffBit() const {
119	std::vector<int> result(N_SELECTIONTYPES);
120	for (int i = 0; i < N_SELECTIONTYPES; i++)
121	result[i] = bitsets_[i].firstOffBit();
122	return result;
123	}
124
125	std::vector<int> SelectionSet::nextOffBit(std::vector<int> fromIndex) const {
126	std::vector<int> result(N_SELECTIONTYPES);
127	for (int i = 0; i < N_SELECTIONTYPES; i++)
128	result[i] = bitsets_[i].nextOffBit(fromIndex[i]);
129	return result;
130	}
131
132	std::vector<int> SelectionSet::firstOnBit() const {
133	std::vector<int> result(N_SELECTIONTYPES);
134	for (int i = 0; i < N_SELECTIONTYPES; i++)
135	result[i] = bitsets_[i].firstOnBit();
136	return result;
137	}
138
139	std::vector<int> SelectionSet::nextOnBit(std::vector<int> fromIndex) const {
140	std::vector<int> result(N_SELECTIONTYPES);
141	for (int i = 0; i < N_SELECTIONTYPES; i++)
142	result[i] = bitsets_[i].nextOnBit(fromIndex[i]);
143	return result;
144	}
145
146	void SelectionSet::andOperator (const SelectionSet& ss) {
147	for (int i = 0; i < N_SELECTIONTYPES; i++)
148	bitsets_[i] &= ss.bitsets_[i];
149	}
150
151	void SelectionSet::orOperator (const SelectionSet& ss) {
152	for (int i = 0; i < N_SELECTIONTYPES; i++)
153	bitsets_[i] \|= ss.bitsets_[i];
154	}
155
156	void SelectionSet::xorOperator (const SelectionSet& ss) {
157	for (int i = 0; i < N_SELECTIONTYPES; i++)
158	bitsets_[i] ^= ss.bitsets_[i];
159	}
160
161	//void SelectionSet::setBits(std::vector<int> fromIndex,
162	// std::vector<int> toIndex, bool value) {
163	// for (int i = 0; i < N_SELECTIONTYPES; i++)
164	// bitsets_[i].setBits(fromIndex[i], toIndex[i], value);
165	//}
166
167	void SelectionSet::clearAll() {
168	for (int i = 0; i < N_SELECTIONTYPES; i++)
169	bitsets_[i].clearAll();
170	}
171
172	void SelectionSet::setAll() {
173	for (int i = 0; i < N_SELECTIONTYPES; i++)
174	bitsets_[i].setAll();
175	}
176
177	std::vector<int> SelectionSet::size() const {
178	std::vector<int> result(N_SELECTIONTYPES);
179	for (int i = 0; i < N_SELECTIONTYPES; i++)
180	result[i] = bitsets_[i].size();
181	return result;
182	}
183
184	void SelectionSet::resize(std::vector<int> nbits) {
185	for (int i = 0; i < N_SELECTIONTYPES; i++)
186	bitsets_[i].resize(nbits[i]);
187	}
188
189	SelectionSet operator\| (const SelectionSet& ss1, const SelectionSet& ss2) {
190	SelectionSet result(ss1);
191	for (int i = 0; i < N_SELECTIONTYPES; i++)
192	result.bitsets_[i] \|= ss2.bitsets_[i];
193	return result;
194	}
195
196	SelectionSet operator& (const SelectionSet& ss1, const SelectionSet& ss2) {
197	SelectionSet result(ss1);
198	for (int i = 0; i < N_SELECTIONTYPES; i++)
199	result.bitsets_[i] &= ss2.bitsets_[i];
200	return result;
201	}
202
203	SelectionSet operator^ (const SelectionSet& ss1, const SelectionSet& ss2) {
204	SelectionSet result(ss1);
205	for (int i = 0; i < N_SELECTIONTYPES; i++)
206	result.bitsets_[i] ^= ss2.bitsets_[i];
207	return result;
208	}
209
210	SelectionSet operator- (const SelectionSet& ss1, const SelectionSet& ss2) {
211	SelectionSet result(ss1);
212	for (int i = 0; i < N_SELECTIONTYPES; i++)
213	result.bitsets_[i] -= ss2.bitsets_[i];
214	return result;
215	}
216
217	bool operator== (const SelectionSet & ss1, const SelectionSet &ss2) {
218
219	for (int i = 0; i < N_SELECTIONTYPES; i++) {
220	assert(ss1.bitsets_[i].size() == ss2.bitsets_[i].size());
221	if (!(ss1.bitsets_[i] == ss2.bitsets_[i])) return false;
222	}
223
224	return true;
225	}
226
227	SelectionSet SelectionSet::parallelReduce() {
228
229	SelectionSet result;
230	for (int i = 0; i < N_SELECTIONTYPES; i++)
231	result.bitsets_[i] = bitsets_[i].parallelReduce();
232
233	return result;
234	}
235
236
237
238	//std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
239	//
240	// return is;
241	//}
242
243	std::ostream& operator<< ( std::ostream& os, const SelectionSet& ss) {
244	for (int i = 0; i < N_SELECTIONTYPES; i++)
245	os << "SelectionSet[" << i << "] = " << ss.bitsets_[i] << std::endl;
246	return os;
247	}
248
249	//void SelectionSet::setBit(std::vector<int> bitIndex, bool value) {
250	// for (int i = 0; i < N_SELECTIONTYPES; i++)
251	// bitsets_[i].setBit(bitIndex[i], value);
252	//}
253
254	}