src/selection/SelectionSet.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 SELECTION_SELECTIONSET_HPP
#define SELECTION_SELECTIONSET_HPP

#include <iostream>
#include <vector>
#include "utils/OpenMDBitSet.hpp"

namespace OpenMD {

  /** 
   * The SelectionType enum.
   *
   * This is used to sort different types of selections by object type
   */
  enum SelectionType {
    STUNTDOUBLE = 0,     /**< StuntDoubles (Atoms & RigidBodies) */
    BOND = 1,            /**< Bonds */
    BEND = 2,            /**< Bends */
    TORSION = 3,         /**< Torsions */
    INVERSION = 4,       /**< Inversions */
    MOLECULE = 5,        /**< Molecules */
    N_SELECTIONTYPES = 6
  };

  class SelectionSet {
  public:
    /** */
    SelectionSet() { bitsets_.resize(N_SELECTIONTYPES); }
    /** */
    SelectionSet(std::vector<int> nbits);

    /** Returns the number of bits set to true in this SelectionSet.  */
    std::vector<int> countBits();

    /** Sets the bit at the specified index to to the complement of its current value. */
    void flip(std::vector<int> bitIndex);
 
    /** Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value. */
    void flip(std::vector<int> fromIndex, std::vector<int> toIndex); 

    /** Sets each bit to the complement of its current value. */
    void flip();
        
    /** Returns the value of the bit with the specified index. */
    std::vector<bool> get(std::vector<int> bitIndex);
        
    /** Returns a new SelectionSet composed of bits from this SelectionSet from fromIndex(inclusive) to toIndex(exclusive). */
    SelectionSet get(std::vector<int> fromIndex, std::vector<int> toIndex); 
        
    /** Returns true if any bits are set to true */
    std::vector<bool> any();

    /** Returns true if no bits are set to true */
    std::vector<bool> none();

    std::vector<int> firstOffBit() const;
        
    /** Returns the index of the first bit that is set to false that occurs on or after the specified starting index.*/
    std::vector<int> nextOffBit(std::vector<int> fromIndex) const; 

    std::vector<int> firstOnBit() const;
        
    /** Returns the index of the first bit that is set to true that occurs on or after the specified starting index. */
    std::vector<int> nextOnBit(std::vector<int> fromIndex) const; 
        
    /** Performs a logical AND of this target bit set with the argument bit set. */
    void andOperator (const SelectionSet& bs);
       
    /** Performs a logical OR of this bit set with the bit set argument. */
    void orOperator (const SelectionSet& bs); 
        
    /** Performs a logical XOR of this bit set with the bit set argument. */
    void xorOperator (const SelectionSet& bs);        
               
    void setBitOn(std::vector<int> bitIndex);

    void setBitOff(std::vector<int> bitIndex);

    //void setRangeOn(std::vector<int> fromIndex, std::vector<int> toIndex) {  setBits(fromIndex, toIndex, true);  }

    //void setRangeOff(std::vector<int> fromIndex, std::vector<int> toIndex) {  setBits(fromIndex, toIndex, false);  }        

    /** Sets all of the bits in this SelectionSet to false. */
    void clearAll();

    void setAll();
        
    /** Returns the number of bits of space actually in use by this SelectionSet to represent bit values. */
    std::vector<int> size() const;

    /** Changes the size of SelectionSet*/
    void resize(std::vector<int> nbits);
        
    SelectionSet& operator&= (const SelectionSet &ss) {  andOperator (ss); return *this; }
    SelectionSet& operator|= (const SelectionSet &ss) { orOperator (ss); return *this; }
    SelectionSet& operator^= (const SelectionSet &ss) { xorOperator (ss); return *this; }
    SelectionSet& operator-= (const SelectionSet &ss) { 
      SelectionSet tmp = *this ^ ss;
      *this &= tmp;
      return *this;
    }

    SelectionSet parallelReduce();
        
    std::vector<bool>  operator[] (std::vector<int> bitIndex)  const {  
      std::vector<bool> result(N_SELECTIONTYPES);
      for (int i = 0; i < N_SELECTIONTYPES; i++) 
        result[i] = bitsets_[i][bitIndex[i]];
      return result;
    }

    friend SelectionSet operator| (const SelectionSet& bs1, const SelectionSet& bs2);
    friend SelectionSet operator& (const SelectionSet& bs1, const SelectionSet& bs2);
    friend SelectionSet operator^ (const SelectionSet& bs1, const SelectionSet& bs2);
    friend SelectionSet operator- (const SelectionSet& bs1, const SelectionSet& bs2);
        
    friend bool operator== (const SelectionSet & bs1, const SelectionSet &bs2);

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

    std::vector<OpenMDBitSet> bitsets_;

    
  private:

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

  };


}
#endif
Revision:	2052
Committed:	Fri Jan 9 19:06:35 2015 UTC (10 years, 7 months ago) by gezelter
File size:	7328 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	User	Rev	Content
1	gezelter	1953	/*
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 SELECTION_SELECTIONSET_HPP
44			#define SELECTION_SELECTIONSET_HPP
45
46			#include <iostream>
47			#include <vector>
48			#include "utils/OpenMDBitSet.hpp"
49
50			namespace OpenMD {
51
52			/**
53			* The SelectionType enum.
54			*
55			* This is used to sort different types of selections by object type
56			*/
57			enum SelectionType {
58			STUNTDOUBLE = 0, /*< StuntDoubles (Atoms & RigidBodies) /
59			BOND = 1, /*< Bonds /
60			BEND = 2, /*< Bends /
61			TORSION = 3, /*< Torsions /
62			INVERSION = 4, /*< Inversions /
63	gezelter	2052	MOLECULE = 5, /*< Molecules /
64			N_SELECTIONTYPES = 6
65	gezelter	1953	};
66
67			class SelectionSet {
68			public:
69			/** */
70			SelectionSet() { bitsets_.resize(N_SELECTIONTYPES); }
71			/** */
72			SelectionSet(std::vector<int> nbits);
73
74			/** Returns the number of bits set to true in this SelectionSet. */
75			std::vector<int> countBits();
76
77			/** Sets the bit at the specified index to to the complement of its current value. */
78			void flip(std::vector<int> bitIndex);
79
80			/** Sets each bit from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the complement of its current value. */
81			void flip(std::vector<int> fromIndex, std::vector<int> toIndex);
82
83			/** Sets each bit to the complement of its current value. */
84			void flip();
85
86			/** Returns the value of the bit with the specified index. */
87			std::vector<bool> get(std::vector<int> bitIndex);
88
89			/** Returns a new SelectionSet composed of bits from this SelectionSet from fromIndex(inclusive) to toIndex(exclusive). */
90			SelectionSet get(std::vector<int> fromIndex, std::vector<int> toIndex);
91
92			/** Returns true if any bits are set to true */
93			std::vector<bool> any();
94
95			/** Returns true if no bits are set to true */
96			std::vector<bool> none();
97
98			std::vector<int> firstOffBit() const;
99
100			/** Returns the index of the first bit that is set to false that occurs on or after the specified starting index.*/
101			std::vector<int> nextOffBit(std::vector<int> fromIndex) const;
102
103			std::vector<int> firstOnBit() const;
104
105			/** Returns the index of the first bit that is set to true that occurs on or after the specified starting index. */
106			std::vector<int> nextOnBit(std::vector<int> fromIndex) const;
107
108			/** Performs a logical AND of this target bit set with the argument bit set. */
109			void andOperator (const SelectionSet& bs);
110
111			/** Performs a logical OR of this bit set with the bit set argument. */
112			void orOperator (const SelectionSet& bs);
113
114			/** Performs a logical XOR of this bit set with the bit set argument. */
115			void xorOperator (const SelectionSet& bs);
116
117			void setBitOn(std::vector<int> bitIndex);
118
119			void setBitOff(std::vector<int> bitIndex);
120
121			//void setRangeOn(std::vector<int> fromIndex, std::vector<int> toIndex) { setBits(fromIndex, toIndex, true); }
122
123			//void setRangeOff(std::vector<int> fromIndex, std::vector<int> toIndex) { setBits(fromIndex, toIndex, false); }
124
125			/** Sets all of the bits in this SelectionSet to false. */
126			void clearAll();
127
128			void setAll();
129
130			/** Returns the number of bits of space actually in use by this SelectionSet to represent bit values. */
131			std::vector<int> size() const;
132
133			/** Changes the size of SelectionSet*/
134			void resize(std::vector<int> nbits);
135
136			SelectionSet& operator&= (const SelectionSet &ss) { andOperator (ss); return *this; }
137			SelectionSet& operator\|= (const SelectionSet &ss) { orOperator (ss); return *this; }
138			SelectionSet& operator^= (const SelectionSet &ss) { xorOperator (ss); return *this; }
139			SelectionSet& operator-= (const SelectionSet &ss) {
140			SelectionSet tmp = *this ^ ss;
141			*this &= tmp;
142			return *this;
143			}
144
145			SelectionSet parallelReduce();
146
147			std::vector<bool> operator[] (std::vector<int> bitIndex) const {
148			std::vector<bool> result(N_SELECTIONTYPES);
149			for (int i = 0; i < N_SELECTIONTYPES; i++)
150			result[i] = bitsets_[i][bitIndex[i]];
151			return result;
152			}
153
154			friend SelectionSet operator\| (const SelectionSet& bs1, const SelectionSet& bs2);
155			friend SelectionSet operator& (const SelectionSet& bs1, const SelectionSet& bs2);
156			friend SelectionSet operator^ (const SelectionSet& bs1, const SelectionSet& bs2);
157			friend SelectionSet operator- (const SelectionSet& bs1, const SelectionSet& bs2);
158
159			friend bool operator== (const SelectionSet & bs1, const SelectionSet &bs2);
160
161			//friend std::istream& operator>> ( std::istream&, const SelectionSet& bs);
162			friend std::ostream& operator<< ( std::ostream&, const SelectionSet& bs) ;
163
164			std::vector<OpenMDBitSet> bitsets_;
165
166
167
168			private:
169
170			/** Sets the bit at the specified index to the specified value. */
171			//void setBit(std::vector<int> bitIndex, bool value);
172
173			/** Sets the bits from the specified fromIndex(inclusive) to the specified toIndex(exclusive) to the specified value. */
174			//void setBits(std::vector<int> fromIndex, std::vector<int> toIndex, bool value);
175
176
177			};
178
179
180			}
181			#endif