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, 234107 (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 <iterator>

#include "utils/OpenMDBitSet.hpp"
#include "utils/Algorithm.hpp"
#ifdef IS_MPI
#include <mpi.h>
#endif

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<bool>::iterator first = bitset_.begin() + fromIndex;
    std::vector<bool>::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<bool>::iterator first = bitset_.begin() + fromIndex;
    std::vector<bool>::iterator last = bitset_.begin() + toIndex;

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

  bool OpenMDBitSet::none() {
    std::vector<bool>::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<bool>::iterator first = bitset_.begin() + fromIndex;
    std::vector<bool>::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());
  }  

  OpenMDBitSet OpenMDBitSet::parallelReduce() {
    OpenMDBitSet result;

#ifdef IS_MPI

    // This is necessary because std::vector<bool> isn't really a
    // std::vector, so we can't pass the address of the first element
    // to the MPI call that follows.  We first have to convert to a
    // std::vector<int> to do the logical_or Allreduce call, then back
    // convert it into the vector<bool>.

    std::vector<int> bsInt(bitset_.begin(), bitset_.end());

    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bsInt[0], 
                              bsInt.size(), MPI::INT, MPI::LOR);

    std::transform(bsInt.begin(), bsInt.end(), 
                   std::back_inserter( result.bitset_ ), to_bool<int>());
#else

    // Not in MPI?  Just return a copy of the current bitset:
    std::copy(bitset_.begin(), bitset_.end(), 
              std::back_inserter( result.bitset_ ));
#endif

    return result;
  }

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

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

}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	7815 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [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	gezelter	1782	#include <iterator>
47	gezelter	1390
48			#include "utils/OpenMDBitSet.hpp"
49			#include "utils/Algorithm.hpp"
50	gezelter	1802	#ifdef IS_MPI
51			#include <mpi.h>
52			#endif
53	gezelter	1390
54			namespace OpenMD {
55			int OpenMDBitSet::countBits() {
56			#ifdef __RWSTD
57			//For the compiler(Sun, MSVC6.0) binding with RougeWave STL Library, we need to use old-style
58			// std::count which is error-prone.
59			int count = 0;
60			std::count(bitset_.begin(), bitset_.end(), true, count);
61			return count;
62			#else
63			return std::count(bitset_.begin(), bitset_.end(), true);
64			#endif
65			}
66
67			void OpenMDBitSet::flip(int fromIndex, int toIndex) {
68			assert(fromIndex <= toIndex);
69			assert(fromIndex >=0);
70			assert(toIndex <= size());
71	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
72			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
73	gezelter	1390
74			std::transform(first, last, first, std::logical_not<bool>());
75
76			}
77
78			OpenMDBitSet OpenMDBitSet::get(int fromIndex, int toIndex) {
79			assert(fromIndex <= toIndex);
80			assert(fromIndex >=0);
81			assert(toIndex <= size());
82	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
83			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
84	gezelter	1390
85			OpenMDBitSet result;
86			std::copy(first, last, std::back_inserter(result.bitset_));
87			return result;
88			}
89
90			bool OpenMDBitSet::none() {
91	gezelter	1782	std::vector<bool>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
92	gezelter	1390	return i == bitset_.end() ? true : false;
93			}
94
95			int OpenMDBitSet::nextOffBit(int fromIndex) const {
96			if (fromIndex <= -1) {
97			//in case -1 or other negative number is passed to this function
98			return -1;
99			}
100
101			++fromIndex;
102			while (fromIndex < size()) {
103			if (!bitset_[fromIndex]) {
104			return fromIndex;
105			}
106			++fromIndex;
107			}
108
109			return -1;
110			}
111
112			int OpenMDBitSet::nextOnBit(int fromIndex) const {
113			if (fromIndex <= -1) {
114			//in case -1 or other negative number is passed to this function
115			return -1;
116			}
117
118			++fromIndex;
119			while (fromIndex < size()) {
120			if (bitset_[fromIndex]) {
121			return fromIndex;
122			}
123			++fromIndex;
124			}
125
126			return -1;
127			}
128
129			void OpenMDBitSet::andOperator (const OpenMDBitSet& bs) {
130			assert(size() == bs.size());
131
132			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_and<bool>());
133			}
134
135			void OpenMDBitSet::orOperator (const OpenMDBitSet& bs) {
136			assert(size() == bs.size());
137			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_or<bool>());
138			}
139
140			void OpenMDBitSet::xorOperator (const OpenMDBitSet& bs) {
141			assert(size() == bs.size());
142			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), OpenMD::logical_xor<bool>());
143			}
144
145			void OpenMDBitSet::setBits(int fromIndex, int toIndex, bool value) {
146			assert(fromIndex <= toIndex);
147			assert(fromIndex >=0);
148			assert(toIndex <= size());
149	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
150			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
151	gezelter	1390	std::fill(first, last, value);
152			}
153
154			void OpenMDBitSet::resize(int nbits) {
155			int oldSize = size();
156			bitset_.resize(nbits);
157			if (nbits > oldSize) {
158			std::fill(bitset_.begin()+oldSize, bitset_.end(), false);
159			}
160			}
161
162			OpenMDBitSet operator\| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
163			assert(bs1.size() == bs2.size());
164
165			OpenMDBitSet result(bs1);
166			result \|= bs2;
167			return result;
168			}
169
170			OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
171			assert(bs1.size() == bs2.size());
172
173			OpenMDBitSet result(bs1);
174			result &= bs2;
175			return result;
176			}
177
178			OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
179			assert(bs1.size() == bs2.size());
180
181			OpenMDBitSet result(bs1);
182			result ^= bs2;
183			return result;
184			}
185
186			OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
187			assert(bs1.size() == bs2.size());
188
189			OpenMDBitSet result(bs1);
190			result -= bs2;
191			return result;
192			}
193
194			bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2) {
195			assert(bs1.size() == bs2.size());
196			return std::equal(bs1.bitset_.begin(), bs1.bitset_.end(), bs2.bitset_.begin());
197	gezelter	1802	}
198
199			OpenMDBitSet OpenMDBitSet::parallelReduce() {
200			OpenMDBitSet result;
201
202			#ifdef IS_MPI
203
204			// This is necessary because std::vector<bool> isn't really a
205			// std::vector, so we can't pass the address of the first element
206			// to the MPI call that follows. We first have to convert to a
207			// std::vector<int> to do the logical_or Allreduce call, then back
208			// convert it into the vector<bool>.
209
210			std::vector<int> bsInt(bitset_.begin(), bitset_.end());
211
212			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bsInt[0],
213			bsInt.size(), MPI::INT, MPI::LOR);
214
215			std::transform(bsInt.begin(), bsInt.end(),
216			std::back_inserter( result.bitset_ ), to_bool<int>());
217			#else
218
219			// Not in MPI? Just return a copy of the current bitset:
220			std::copy(bitset_.begin(), bitset_.end(),
221			std::back_inserter( result.bitset_ ));
222			#endif
223
224			return result;
225	gezelter	1390	}
226
227			//std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
228			//
229			// return is;
230			//}
231
232			std::ostream& operator<< ( std::ostream& os, const OpenMDBitSet& bs) {
233	gezelter	1782	for (unsigned int i = 0; i < bs.bitset_.size(); ++i) {
234	gezelter	1390	std::string val = bs[i] ? "true" : "false";
235			os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
236			}
237
238			return os;
239			}
240
241			}