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
#	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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
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	}