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]  Vardeman & Gezelter, in progress (2009).                        
 */

#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:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	6766 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	#include <algorithm>
43	#include <cassert>
44	#include <string>
45
46	#include "utils/OpenMDBitSet.hpp"
47	#include "utils/Algorithm.hpp"
48
49	namespace OpenMD {
50	int OpenMDBitSet::countBits() {
51	#ifdef __RWSTD
52	//For the compiler(Sun, MSVC6.0) binding with RougeWave STL Library, we need to use old-style
53	// std::count which is error-prone.
54	int count = 0;
55	std::count(bitset_.begin(), bitset_.end(), true, count);
56	return count;
57	#else
58	return std::count(bitset_.begin(), bitset_.end(), true);
59	#endif
60	}
61
62	void OpenMDBitSet::flip(int fromIndex, int toIndex) {
63	assert(fromIndex <= toIndex);
64	assert(fromIndex >=0);
65	assert(toIndex <= size());
66	std::vector<char>::iterator first = bitset_.begin() + fromIndex;
67	std::vector<char>::iterator last = bitset_.begin() + toIndex;
68
69	std::transform(first, last, first, std::logical_not<bool>());
70
71	}
72
73	OpenMDBitSet OpenMDBitSet::get(int fromIndex, int toIndex) {
74	assert(fromIndex <= toIndex);
75	assert(fromIndex >=0);
76	assert(toIndex <= size());
77	std::vector<char>::iterator first = bitset_.begin() + fromIndex;
78	std::vector<char>::iterator last = bitset_.begin() + toIndex;
79
80	OpenMDBitSet result;
81	std::copy(first, last, std::back_inserter(result.bitset_));
82	return result;
83	}
84
85	bool OpenMDBitSet::none() {
86	std::vector<char>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
87	return i == bitset_.end() ? true : false;
88	}
89
90	int OpenMDBitSet::nextOffBit(int fromIndex) const {
91	if (fromIndex <= -1) {
92	//in case -1 or other negative number is passed to this function
93	return -1;
94	}
95
96	++fromIndex;
97	while (fromIndex < size()) {
98	if (!bitset_[fromIndex]) {
99	return fromIndex;
100	}
101	++fromIndex;
102	}
103
104	return -1;
105	}
106
107	int OpenMDBitSet::nextOnBit(int fromIndex) const {
108	if (fromIndex <= -1) {
109	//in case -1 or other negative number is passed to this function
110	return -1;
111	}
112
113	++fromIndex;
114	while (fromIndex < size()) {
115	if (bitset_[fromIndex]) {
116	return fromIndex;
117	}
118	++fromIndex;
119	}
120
121	return -1;
122	}
123
124	void OpenMDBitSet::andOperator (const OpenMDBitSet& bs) {
125	assert(size() == bs.size());
126
127	std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_and<bool>());
128	}
129
130	void OpenMDBitSet::orOperator (const OpenMDBitSet& bs) {
131	assert(size() == bs.size());
132	std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_or<bool>());
133	}
134
135	void OpenMDBitSet::xorOperator (const OpenMDBitSet& bs) {
136	assert(size() == bs.size());
137	std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), OpenMD::logical_xor<bool>());
138	}
139
140	void OpenMDBitSet::setBits(int fromIndex, int toIndex, bool value) {
141	assert(fromIndex <= toIndex);
142	assert(fromIndex >=0);
143	assert(toIndex <= size());
144	std::vector<char>::iterator first = bitset_.begin() + fromIndex;
145	std::vector<char>::iterator last = bitset_.begin() + toIndex;
146	std::fill(first, last, value);
147	}
148
149	void OpenMDBitSet::resize(int nbits) {
150	int oldSize = size();
151	bitset_.resize(nbits);
152	if (nbits > oldSize) {
153	std::fill(bitset_.begin()+oldSize, bitset_.end(), false);
154	}
155	}
156
157	OpenMDBitSet operator\| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
158	assert(bs1.size() == bs2.size());
159
160	OpenMDBitSet result(bs1);
161	result \|= bs2;
162	return result;
163	}
164
165	OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
166	assert(bs1.size() == bs2.size());
167
168	OpenMDBitSet result(bs1);
169	result &= bs2;
170	return result;
171	}
172
173	OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
174	assert(bs1.size() == bs2.size());
175
176	OpenMDBitSet result(bs1);
177	result ^= bs2;
178	return result;
179	}
180
181	OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
182	assert(bs1.size() == bs2.size());
183
184	OpenMDBitSet result(bs1);
185	result -= bs2;
186	return result;
187	}
188
189	bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2) {
190	assert(bs1.size() == bs2.size());
191	return std::equal(bs1.bitset_.begin(), bs1.bitset_.end(), bs2.bitset_.begin());
192	}
193
194	//std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
195	//
196	// return is;
197	//}
198
199	std::ostream& operator<< ( std::ostream& os, const OpenMDBitSet& bs) {
200	for (int i = 0; i < bs.bitset_.size(); ++i) {
201	std::string val = bs[i] ? "true" : "false";
202	os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
203	}
204
205	return os;
206	}
207
208	}