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).
 */

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

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

#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<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:	1938
Committed:	Thu Oct 31 15:32:17 2013 UTC (11 years, 6 months ago) by gezelter
File size:	7816 byte(s)
Log Message:	Some MPI include re-ordering to work with the Intel MPI implementation.
#	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	gezelter	1938	#ifdef IS_MPI
44			#include <mpi.h>
45			#endif
46
47	gezelter	1390	#include <algorithm>
48			#include <cassert>
49			#include <string>
50	gezelter	1782	#include <iterator>
51	gezelter	1390
52			#include "utils/OpenMDBitSet.hpp"
53			#include "utils/Algorithm.hpp"
54
55			namespace OpenMD {
56			int OpenMDBitSet::countBits() {
57			#ifdef __RWSTD
58			//For the compiler(Sun, MSVC6.0) binding with RougeWave STL Library, we need to use old-style
59			// std::count which is error-prone.
60			int count = 0;
61			std::count(bitset_.begin(), bitset_.end(), true, count);
62			return count;
63			#else
64			return std::count(bitset_.begin(), bitset_.end(), true);
65			#endif
66			}
67
68			void OpenMDBitSet::flip(int fromIndex, int toIndex) {
69			assert(fromIndex <= toIndex);
70			assert(fromIndex >=0);
71			assert(toIndex <= size());
72	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
73			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
74	gezelter	1390
75			std::transform(first, last, first, std::logical_not<bool>());
76
77			}
78
79			OpenMDBitSet OpenMDBitSet::get(int fromIndex, int toIndex) {
80			assert(fromIndex <= toIndex);
81			assert(fromIndex >=0);
82			assert(toIndex <= size());
83	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
84			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
85	gezelter	1390
86			OpenMDBitSet result;
87			std::copy(first, last, std::back_inserter(result.bitset_));
88			return result;
89			}
90
91			bool OpenMDBitSet::none() {
92	gezelter	1782	std::vector<bool>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
93	gezelter	1390	return i == bitset_.end() ? true : false;
94			}
95
96			int OpenMDBitSet::nextOffBit(int fromIndex) const {
97			if (fromIndex <= -1) {
98			//in case -1 or other negative number is passed to this function
99			return -1;
100			}
101
102			++fromIndex;
103			while (fromIndex < size()) {
104			if (!bitset_[fromIndex]) {
105			return fromIndex;
106			}
107			++fromIndex;
108			}
109
110			return -1;
111			}
112
113			int OpenMDBitSet::nextOnBit(int fromIndex) const {
114			if (fromIndex <= -1) {
115			//in case -1 or other negative number is passed to this function
116			return -1;
117			}
118
119			++fromIndex;
120			while (fromIndex < size()) {
121			if (bitset_[fromIndex]) {
122			return fromIndex;
123			}
124			++fromIndex;
125			}
126
127			return -1;
128			}
129
130			void OpenMDBitSet::andOperator (const OpenMDBitSet& bs) {
131			assert(size() == bs.size());
132
133			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_and<bool>());
134			}
135
136			void OpenMDBitSet::orOperator (const OpenMDBitSet& bs) {
137			assert(size() == bs.size());
138			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), std::logical_or<bool>());
139			}
140
141			void OpenMDBitSet::xorOperator (const OpenMDBitSet& bs) {
142			assert(size() == bs.size());
143			std::transform(bs.bitset_.begin(), bs.bitset_.end(), bitset_.begin(), bitset_.begin(), OpenMD::logical_xor<bool>());
144			}
145
146			void OpenMDBitSet::setBits(int fromIndex, int toIndex, bool value) {
147			assert(fromIndex <= toIndex);
148			assert(fromIndex >=0);
149			assert(toIndex <= size());
150	gezelter	1782	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
151			std::vector<bool>::iterator last = bitset_.begin() + toIndex;
152	gezelter	1390	std::fill(first, last, value);
153			}
154
155			void OpenMDBitSet::resize(int nbits) {
156			int oldSize = size();
157			bitset_.resize(nbits);
158			if (nbits > oldSize) {
159			std::fill(bitset_.begin()+oldSize, bitset_.end(), false);
160			}
161			}
162
163			OpenMDBitSet operator\| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
164			assert(bs1.size() == bs2.size());
165
166			OpenMDBitSet result(bs1);
167			result \|= bs2;
168			return result;
169			}
170
171			OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
172			assert(bs1.size() == bs2.size());
173
174			OpenMDBitSet result(bs1);
175			result &= bs2;
176			return result;
177			}
178
179			OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
180			assert(bs1.size() == bs2.size());
181
182			OpenMDBitSet result(bs1);
183			result ^= bs2;
184			return result;
185			}
186
187			OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2) {
188			assert(bs1.size() == bs2.size());
189
190			OpenMDBitSet result(bs1);
191			result -= bs2;
192			return result;
193			}
194
195			bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2) {
196			assert(bs1.size() == bs2.size());
197			return std::equal(bs1.bitset_.begin(), bs1.bitset_.end(), bs2.bitset_.begin());
198	gezelter	1802	}
199
200			OpenMDBitSet OpenMDBitSet::parallelReduce() {
201			OpenMDBitSet result;
202
203			#ifdef IS_MPI
204
205			// This is necessary because std::vector<bool> isn't really a
206			// std::vector, so we can't pass the address of the first element
207			// to the MPI call that follows. We first have to convert to a
208			// std::vector<int> to do the logical_or Allreduce call, then back
209			// convert it into the vector<bool>.
210
211			std::vector<int> bsInt(bitset_.begin(), bitset_.end());
212
213			MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bsInt[0],
214			bsInt.size(), MPI::INT, MPI::LOR);
215
216			std::transform(bsInt.begin(), bsInt.end(),
217			std::back_inserter( result.bitset_ ), to_bool<int>());
218			#else
219
220			// Not in MPI? Just return a copy of the current bitset:
221			std::copy(bitset_.begin(), bitset_.end(),
222			std::back_inserter( result.bitset_ ));
223			#endif
224
225			return result;
226	gezelter	1390	}
227
228			//std::istream& operator>> ( std::istream& is, const OpenMDBitSet& bs) {
229			//
230			// return is;
231			//}
232
233			std::ostream& operator<< ( std::ostream& os, const OpenMDBitSet& bs) {
234	gezelter	1782	for (unsigned int i = 0; i < bs.bitset_.size(); ++i) {
235	gezelter	1390	std::string val = bs[i] ? "true" : "false";
236			os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
237			}
238
239			return os;
240			}
241
242			}