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_Allreduce(MPI_IN_PLACE, &bsInt[0], 
                  bsInt.size(), MPI_INT, MPI_LOR, MPI_COMM_WORLD);

    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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 2 months ago) by gezelter
File size:	7805 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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, 234107 (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	#ifdef IS_MPI
44	#include <mpi.h>
45	#endif
46
47	#include <algorithm>
48	#include <cassert>
49	#include <string>
50	#include <iterator>
51
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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
73	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
74
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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
84	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
85
86	OpenMDBitSet result;
87	std::copy(first, last, std::back_inserter(result.bitset_));
88	return result;
89	}
90
91	bool OpenMDBitSet::none() {
92	std::vector<bool>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
93	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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
151	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
152	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	}
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_Allreduce(MPI_IN_PLACE, &bsInt[0],
214	bsInt.size(), MPI_INT, MPI_LOR, MPI_COMM_WORLD);
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	}
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	for (unsigned int i = 0; i < bs.bitset_.size(); ++i) {
235	std::string val = bs[i] ? "true" : "false";
236	os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
237	}
238
239	return os;
240	}
241
242	}