src/utils/OpenMDBitSet.hpp

/*
 * 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).
 */

#ifndef UTILS_OPENMDBITSET_HPP
#define UTILS_OPENMDBITSET_HPP

#include <iostream>
#include <vector>
namespace OpenMD {

  /**
   * @class OpenMDBitSet OpenMDBitSet.hpp "OpenMDBitSet.hpp"
   * @brief OpenMDBitSet is a wrapper class of std::vector<bool> to act as a growable std::bitset 
   */
  class OpenMDBitSet {
  public:
    /** */
    OpenMDBitSet() {}
    /** */
    OpenMDBitSet(int nbits) : bitset_(nbits) {clearAll(); }

    /** Returns the number of bits set to true in this OpenMDBitSet.  */
    int countBits();

    /** Sets the bit at the specified index to to the complement of its current value. */
    void flip(int bitIndex) {  bitset_[bitIndex] = !bitset_[bitIndex];  }
 
    /** Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value. */
    void flip(int fromIndex, int toIndex); 

    /** Sets each bit to the complement of its current value. */
    void flip() { flip(0, size()); }
        
    /** Returns the value of the bit with the specified index. */
    bool get(int bitIndex) {  return bitset_[bitIndex];  }
        
    /** Returns a new OpenMDBitSet composed of bits from this OpenMDBitSet from fromIndex(inclusive) to toIndex(exclusive). */
    OpenMDBitSet get(int fromIndex, int toIndex); 
        
    /** Returns true if any bits are set to true */
    bool any() {return !none(); }

    /** Returns true if no bits are set to true */
    bool none();

    int firstOffBit() const { return !bitset_[0] ? 0 : nextOffBit(0); }
        
    /** Returns the index of the first bit that is set to false that occurs on or after the specified starting index.*/
    int nextOffBit(int fromIndex) const; 

    int firstOnBit() const { return bitset_[0] ? 0 : nextOnBit(0); }
        
    /** Returns the index of the first bit that is set to true that occurs on or after the specified starting index. */
    int nextOnBit(int fromIndex) const; 
        
    /** Performs a logical AND of this target bit set with the argument bit set. */
    void andOperator (const OpenMDBitSet& bs);
       
    /** Performs a logical OR of this bit set with the bit set argument. */
    void orOperator (const OpenMDBitSet& bs); 
        
    /** Performs a logical XOR of this bit set with the bit set argument. */
    void xorOperator (const OpenMDBitSet& bs);        
               
    void setBitOn(int bitIndex) {  setBit(bitIndex, true);  }

    void setBitOff(int bitIndex) {  setBit(bitIndex, false);  }

    void setRangeOn(int fromIndex, int toIndex) {  setBits(fromIndex, toIndex, true);  }

    void setRangeOff(int fromIndex, int toIndex) {  setBits(fromIndex, toIndex, false);  }        

    /** Sets all of the bits in this OpenMDBitSet to false. */
    void clearAll() {  setRangeOff(0, size());  }         

    void setAll() {  setRangeOn(0, size());  }        
        
    /** Returns the number of bits of space actually in use by this OpenMDBitSet to represent bit values. */
    int size() const {  return bitset_.size();  }

    /** Changes the size of OpenMDBitSet*/
    void resize(int nbits);
        
    OpenMDBitSet& operator&= (const OpenMDBitSet &bs) {  andOperator (bs); return *this; }
    OpenMDBitSet& operator|= (const OpenMDBitSet &bs) { orOperator (bs); return *this; }
    OpenMDBitSet& operator^= (const OpenMDBitSet &bs) { xorOperator (bs); return *this; }
    OpenMDBitSet& operator-= (const OpenMDBitSet &bs) { 
      OpenMDBitSet tmp = *this ^ bs;
      *this &= tmp;
      return *this;
    }

    OpenMDBitSet parallelReduce();
        
    bool operator[] (int bitIndex)  const {  return bitset_[bitIndex];  }
    friend OpenMDBitSet operator| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
    friend OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
    friend OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
    friend OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
        
    friend bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2);

    //friend std::istream& operator>> ( std::istream&, const OpenMDBitSet& bs);
    friend std::ostream& operator<< ( std::ostream&, const OpenMDBitSet& bs) ;

  private:

    /** Sets the bit at the specified index to the specified value. */
    void setBit(int bitIndex, bool value) { bitset_[bitIndex] = value; }
        
    /** Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the specified value. */
    void setBits(int fromIndex, int toIndex, bool value);
        
    std::vector<bool> bitset_;
  }; 

}
#endif
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	6832 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	#ifndef UTILS_OPENMDBITSET_HPP
44	#define UTILS_OPENMDBITSET_HPP
45
46	#include <iostream>
47	#include <vector>
48	namespace OpenMD {
49
50	/**
51	* @class OpenMDBitSet OpenMDBitSet.hpp "OpenMDBitSet.hpp"
52	* @brief OpenMDBitSet is a wrapper class of std::vector<bool> to act as a growable std::bitset
53	*/
54	class OpenMDBitSet {
55	public:
56	/** */
57	OpenMDBitSet() {}
58	/** */
59	OpenMDBitSet(int nbits) : bitset_(nbits) {clearAll(); }
60
61	/** Returns the number of bits set to true in this OpenMDBitSet. */
62	int countBits();
63
64	/** Sets the bit at the specified index to to the complement of its current value. */
65	void flip(int bitIndex) { bitset_[bitIndex] = !bitset_[bitIndex]; }
66
67	/** Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value. */
68	void flip(int fromIndex, int toIndex);
69
70	/** Sets each bit to the complement of its current value. */
71	void flip() { flip(0, size()); }
72
73	/** Returns the value of the bit with the specified index. */
74	bool get(int bitIndex) { return bitset_[bitIndex]; }
75
76	/** Returns a new OpenMDBitSet composed of bits from this OpenMDBitSet from fromIndex(inclusive) to toIndex(exclusive). */
77	OpenMDBitSet get(int fromIndex, int toIndex);
78
79	/** Returns true if any bits are set to true */
80	bool any() {return !none(); }
81
82	/** Returns true if no bits are set to true */
83	bool none();
84
85	int firstOffBit() const { return !bitset_[0] ? 0 : nextOffBit(0); }
86
87	/** Returns the index of the first bit that is set to false that occurs on or after the specified starting index.*/
88	int nextOffBit(int fromIndex) const;
89
90	int firstOnBit() const { return bitset_[0] ? 0 : nextOnBit(0); }
91
92	/** Returns the index of the first bit that is set to true that occurs on or after the specified starting index. */
93	int nextOnBit(int fromIndex) const;
94
95	/** Performs a logical AND of this target bit set with the argument bit set. */
96	void andOperator (const OpenMDBitSet& bs);
97
98	/** Performs a logical OR of this bit set with the bit set argument. */
99	void orOperator (const OpenMDBitSet& bs);
100
101	/** Performs a logical XOR of this bit set with the bit set argument. */
102	void xorOperator (const OpenMDBitSet& bs);
103
104	void setBitOn(int bitIndex) { setBit(bitIndex, true); }
105
106	void setBitOff(int bitIndex) { setBit(bitIndex, false); }
107
108	void setRangeOn(int fromIndex, int toIndex) { setBits(fromIndex, toIndex, true); }
109
110	void setRangeOff(int fromIndex, int toIndex) { setBits(fromIndex, toIndex, false); }
111
112	/** Sets all of the bits in this OpenMDBitSet to false. */
113	void clearAll() { setRangeOff(0, size()); }
114
115	void setAll() { setRangeOn(0, size()); }
116
117	/** Returns the number of bits of space actually in use by this OpenMDBitSet to represent bit values. */
118	int size() const { return bitset_.size(); }
119
120	/** Changes the size of OpenMDBitSet*/
121	void resize(int nbits);
122
123	OpenMDBitSet& operator&= (const OpenMDBitSet &bs) { andOperator (bs); return *this; }
124	OpenMDBitSet& operator\|= (const OpenMDBitSet &bs) { orOperator (bs); return *this; }
125	OpenMDBitSet& operator^= (const OpenMDBitSet &bs) { xorOperator (bs); return *this; }
126	OpenMDBitSet& operator-= (const OpenMDBitSet &bs) {
127	OpenMDBitSet tmp = *this ^ bs;
128	*this &= tmp;
129	return *this;
130	}
131
132	OpenMDBitSet parallelReduce();
133
134	bool operator[] (int bitIndex) const { return bitset_[bitIndex]; }
135	friend OpenMDBitSet operator\| (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
136	friend OpenMDBitSet operator& (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
137	friend OpenMDBitSet operator^ (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
138	friend OpenMDBitSet operator- (const OpenMDBitSet& bs1, const OpenMDBitSet& bs2);
139
140	friend bool operator== (const OpenMDBitSet & bs1, const OpenMDBitSet &bs2);
141
142	//friend std::istream& operator>> ( std::istream&, const OpenMDBitSet& bs);
143	friend std::ostream& operator<< ( std::ostream&, const OpenMDBitSet& bs) ;
144
145	private:
146
147	/** Sets the bit at the specified index to the specified value. */
148	void setBit(int bitIndex, bool value) { bitset_[bitIndex] = value; }
149
150	/** Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the specified value. */
151	void setBits(int fromIndex, int toIndex, bool value);
152
153	std::vector<bool> bitset_;
154	};
155
156	}
157	#endif