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 <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:	1802
Committed:	Wed Oct 3 14:07:28 2012 UTC (13 years, 1 month ago) by gezelter
File size:	7814 byte(s)
Log Message:	Parallel fixes for selection syntax (e.g. DistanceFinder).
#	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	#include <iterator>
47
48	#include "utils/OpenMDBitSet.hpp"
49	#include "utils/Algorithm.hpp"
50	#ifdef IS_MPI
51	#include <mpi.h>
52	#endif
53
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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
72	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
73
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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
83	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
84
85	OpenMDBitSet result;
86	std::copy(first, last, std::back_inserter(result.bitset_));
87	return result;
88	}
89
90	bool OpenMDBitSet::none() {
91	std::vector<bool>::iterator i = std::find(bitset_.begin(), bitset_.end(), true);
92	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	std::vector<bool>::iterator first = bitset_.begin() + fromIndex;
150	std::vector<bool>::iterator last = bitset_.begin() + toIndex;
151	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	}
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	}
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	for (unsigned int i = 0; i < bs.bitset_.size(); ++i) {
234	std::string val = bs[i] ? "true" : "false";
235	os << "OpenMDBitSet[" << i <<"] = " << val << std::endl;
236	}
237
238	return os;
239	}
240
241	}