src/utils/OpenMDBitSet.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, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */

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

#include "utils/OpenMDBitSet.hpp"
#include "utils/Algorithm.hpp"

namespace OpenMD {
  int OpenMDBitSet::countBits() {
#ifdef __RWSTD    
    //For the compiler(Sun, MSVC6.0) binding with RougeWave STL Library, we need to use old-style
    // std::count which is error-prone.
    int count = 0;
    std::count(bitset_.begin(), bitset_.end(), true, count);
    return count;
#else
    return std::count(bitset_.begin(), bitset_.end(), true);
#endif
  }

  void OpenMDBitSet::flip(int fromIndex, int toIndex) {
    assert(fromIndex <= toIndex);
    assert(fromIndex >=0);
    assert(toIndex <= size());
    std::vector<char>::iterator first = bitset_.begin() + fromIndex;
    std::vector<char>::iterator last = bitset_.begin() + toIndex;

    std::transform(first, last, first, std::logical_not<bool>());
        
  }

  OpenMDBitSet OpenMDBitSet::get(int fromIndex, int toIndex) {
    assert(fromIndex <= toIndex);
    assert(fromIndex >=0);
    assert(toIndex <= size());
    std::vector<char>::iterator first = bitset_.begin() + fromIndex;
    std::vector<char>::iterator last = bitset_.begin() + toIndex;

    OpenMDBitSet result;
    std::copy(first, last, std::back_inserter(result.bitset_));
    return result;
  }

  bool OpenMDBitSet::none() {
    std::vector<char>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
    return i == bitset_.end() ? true : false;
  }
    
  int OpenMDBitSet::nextOffBit(int fromIndex) const {
    if (fromIndex <= -1) {
      //in case -1 or other negative number is passed to this function
      return -1;
    }
    
    ++fromIndex;
    while (fromIndex < size()) {
      if (!bitset_[fromIndex]) {
        return fromIndex;
      }
      ++fromIndex;
    }

    return -1;
  }

  int OpenMDBitSet::nextOnBit(int fromIndex) const {
    if (fromIndex <= -1) {
      //in case -1 or other negative number is passed to this function
      return -1;
    }

    ++fromIndex;
    while (fromIndex < size()) {
      if (bitset_[fromIndex]) {
        return fromIndex;
      }
      ++fromIndex;
    }

    return -1;
  }

  void OpenMDBitSet::andOperator (const OpenMDBitSet& bs) {
    assert(size() == bs.size());

    std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_and<bool>());
  }

  void OpenMDBitSet::orOperator (const OpenMDBitSet& bs) {
    assert(size() == bs.size());
    std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_or<bool>());    
  }

  void OpenMDBitSet::xorOperator (const OpenMDBitSet& bs) {
    assert(size() == bs.size());
    std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), OpenMD::logical_xor<bool>());        
  }
   
  void OpenMDBitSet::setBits(int fromIndex, int toIndex, bool value) {
    assert(fromIndex <= toIndex);
    assert(fromIndex >=0);
    assert(toIndex <= size());
    std::vector<char>::iterator first = bitset_.begin() + fromIndex;
    std::vector<char>::iterator last = bitset_.begin() + toIndex;
    std::fill(first, last, value);
  }

  void OpenMDBitSet::resize(int nbits) {
    int oldSize = size();
    bitset_.resize(nbits);
    if (nbits > oldSize) {
      std::fill(bitset_.begin()+oldSize, bitset_.end(), false);
    }
  }

  OpenMDBitSet operator| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
    assert(bs1.size() == bs2.size());

    OpenMDBitSet result(bs1);
    result |= bs2;
    return result;
  }

  OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
    assert(bs1.size() == bs2.size());

    OpenMDBitSet result(bs1);
    result &= bs2;
    return result;
  }

  OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
    assert(bs1.size() == bs2.size());

    OpenMDBitSet result(bs1);
    result ^= bs2;
    return result;
  }

  OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
    assert(bs1.size() == bs2.size());

    OpenMDBitSet result(bs1);
    result -= bs2;
    return result;
  }

  bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2) {
    assert(bs1.size() == bs2.size());
    return std::equal(bs1.bitset_.begin(), bs1.bitset_.end(), bs2.bitset_.begin());
  }

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

  std::ostream& operator<< ( std::ostream& os, const OpenMDBitSet& bs) {
    for (int i = 0; i < bs.bitset_.size(); ++i) {
      std::string val = bs[i] ? "true" : "false";
      os << "OpenMDBitSet[" << i <<"] = " << val << std::endl; 
    }
    
    return os;
  }

}
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	6832 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	1390	/*
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	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	1390	*/
42
43			#include <algorithm>
44			#include <cassert>
45			#include <string>
46
47			#include "utils/OpenMDBitSet.hpp"
48			#include "utils/Algorithm.hpp"
49
50			namespace OpenMD {
51			int OpenMDBitSet::countBits() {
52			#ifdef __RWSTD
53			//For the compiler(Sun, MSVC6.0) binding with RougeWave STL Library, we need to use old-style
54			// std::count which is error-prone.
55			int count = 0;
56			std::count(bitset_.begin(), bitset_.end(), true, count);
57			return count;
58			#else
59			return std::count(bitset_.begin(), bitset_.end(), true);
60			#endif
61			}
62
63			void OpenMDBitSet::flip(int fromIndex, int toIndex) {
64			assert(fromIndex <= toIndex);
65			assert(fromIndex >=0);
66			assert(toIndex <= size());
67			std::vector<char>::iterator first = bitset_.begin() + fromIndex;
68			std::vector<char>::iterator last = bitset_.begin() + toIndex;
69
70			std::transform(first, last, first, std::logical_not<bool>());
71
72			}
73
74			OpenMDBitSet OpenMDBitSet::get(int fromIndex, int toIndex) {
75			assert(fromIndex <= toIndex);
76			assert(fromIndex >=0);
77			assert(toIndex <= size());
78			std::vector<char>::iterator first = bitset_.begin() + fromIndex;
79			std::vector<char>::iterator last = bitset_.begin() + toIndex;
80
81			OpenMDBitSet result;
82			std::copy(first, last, std::back_inserter(result.bitset_));
83			return result;
84			}
85
86			bool OpenMDBitSet::none() {
87			std::vector<char>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
88			return i == bitset_.end() ? true : false;
89			}
90
91			int OpenMDBitSet::nextOffBit(int fromIndex) const {
92			if (fromIndex <= -1) {
93			//in case -1 or other negative number is passed to this function
94			return -1;
95			}
96
97			++fromIndex;
98			while (fromIndex < size()) {
99			if (!bitset_[fromIndex]) {
100			return fromIndex;
101			}
102			++fromIndex;
103			}
104
105			return -1;
106			}
107
108			int OpenMDBitSet::nextOnBit(int fromIndex) const {
109			if (fromIndex <= -1) {
110			//in case -1 or other negative number is passed to this function
111			return -1;
112			}
113
114			++fromIndex;
115			while (fromIndex < size()) {
116			if (bitset_[fromIndex]) {
117			return fromIndex;
118			}
119			++fromIndex;
120			}
121
122			return -1;
123			}
124
125			void OpenMDBitSet::andOperator (const OpenMDBitSet& bs) {
126			assert(size() == bs.size());
127
128			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_and<bool>());
129			}
130
131			void OpenMDBitSet::orOperator (const OpenMDBitSet& bs) {
132			assert(size() == bs.size());
133			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_or<bool>());
134			}
135
136			void OpenMDBitSet::xorOperator (const OpenMDBitSet& bs) {
137			assert(size() == bs.size());
138			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), OpenMD::logical_xor<bool>());
139			}
140
141			void OpenMDBitSet::setBits(int fromIndex, int toIndex, bool value) {
142			assert(fromIndex <= toIndex);
143			assert(fromIndex >=0);
144			assert(toIndex <= size());
145			std::vector<char>::iterator first = bitset_.begin() + fromIndex;
146			std::vector<char>::iterator last = bitset_.begin() + toIndex;
147			std::fill(first, last, value);
148			}
149
150			void OpenMDBitSet::resize(int nbits) {
151			int oldSize = size();
152			bitset_.resize(nbits);
153			if (nbits > oldSize) {
154			std::fill(bitset_.begin()+oldSize, bitset_.end(), false);
155			}
156			}
157
158			OpenMDBitSet operator\| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
159			assert(bs1.size() == bs2.size());
160
161			OpenMDBitSet result(bs1);
162			result \|= bs2;
163			return result;
164			}
165
166			OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
167			assert(bs1.size() == bs2.size());
168
169			OpenMDBitSet result(bs1);
170			result &= bs2;
171			return result;
172			}
173
174			OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
175			assert(bs1.size() == bs2.size());
176
177			OpenMDBitSet result(bs1);
178			result ^= bs2;
179			return result;
180			}
181
182			OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
183			assert(bs1.size() == bs2.size());
184
185			OpenMDBitSet result(bs1);
186			result -= bs2;
187			return result;
188			}
189
190			bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2) {
191			assert(bs1.size() == bs2.size());
192			return std::equal(bs1.bitset_.begin(), bs1.bitset_.end(), bs2.bitset_.begin());
193			}
194
195			//std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
196			//
197			// return is;
198			//}
199
200			std::ostream& operator<< ( std::ostream& os, const OpenMDBitSet& bs) {
201			for (int i = 0; i < bs.bitset_.size(); ++i) {
202			std::string val = bs[i] ? "true" : "false";
203			os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
204			}
205
206			return os;
207			}
208
209			}