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, 9 months ago) by gezelter
File size:	7328 byte(s)
Log Message:	Updating Hydrogen Bonding structures, and selection syntax to include molecule selections:
#	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 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	MOLECULE = 5, /*< Molecules /
64	N_SELECTIONTYPES = 6
65	};
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