src/primitives/ShortRangeInteraction.hpp

/*
 * Copyright (c) 2013 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 PRIMITIVES_SHORTRANGEINTERACTION_HPP
#define PRIMITIVES_SHORTRANGEINTERACTION_HPP

#include <vector>

#include "visitors/BaseVisitor.hpp"
#include "utils/PropertyMap.hpp"
#include "brains/Snapshot.hpp"
#include "brains/SnapshotManager.hpp"

namespace OpenMD{

  /**
   * @class ShortRangeInteraction 
   * @brief 
   *
   * A ShortRangeInteraction holds some bookeeping data for bonded
   * interactions (e.g. Bonds, Bends, Torsions, Inversions).
   *
   */
  class ShortRangeInteraction{
  public:    

    virtual ~ShortRangeInteraction();
        
    /**
     * Returns the global index of this ShortRangeInteraction.
     * @return  the global index of this ShortRangeInteraction 
     */
    int getGlobalIndex() {
      return globalIndex_;
    }

    /**
     * Sets the global index of this ShortRangeInteraction.
     * @param index new global index to be set
     */
    void setGlobalIndex(int index) {
      globalIndex_ = index;
    }
    
    /** 
     * Returns the local index of this ShortRangeInteraction 
     * @return the local index of this ShortRangeInteraction
     */
    int getLocalIndex() {
      return localIndex_;
    }

    /**
     * Sets the local index of this ShortRangeInteraction
     * @param index new index to be set
     */        
    void setLocalIndex(int index) {
      localIndex_ = index;
    }    


    /**
     * Sets the Snapshot Manager of this ShortRangeInteraction
     */
    void setSnapshotManager(SnapshotManager* sman) {
      snapshotMan_ = sman;
    }


    /** Returns the name of this ShortRangeInteraction */
    virtual std::string getName() = 0;
        
    /** Sets the name of this ShortRangeInteraction*/
    virtual void setName(const std::string& name) {}

    /**
     * <p>
     * The purpose of the Visitor Pattern is to encapsulate an
     * operation that you want to perform on the elements of a data
     * structure. In this way, you can change the operation being
     * performed on a structure without the need of changing the
     * classes of the elements that you are operating on. Using a
     * Visitor pattern allows you to decouple the classes for the data
     * structure and the algorithms used upon them
     * </p>
     * @param v visitor
     */      
    virtual void accept(BaseVisitor* v) = 0;

    /**
     * Returns the previous value of this ShortRangeInteraction
     * @return the value of this ShortRangeInteraction
     */    
    virtual RealType getPrevValue();

    /**
     * Returns the current value of this ShortRangeInteraction
     * @return the current value of this ShortRangeInteraction
     */    
    virtual RealType getValue();

    /**
     * Returns the value of this ShortRangeInteraction in specified snapshot 
     * @return the value of this ShortRangeInteraction
     * @param snapshotNo
     */    
    virtual RealType getValue(int snapshotNo) = 0;

    virtual std::vector<Atom*> getAtoms() { return atoms_; }

    /**
     * Adds property into property map
     * @param genData GenericData to be added into PropertyMap
     */
    void addProperty(GenericData* genData);

    /**
     * Removes property from PropertyMap by name
     * @param propName the name of property to be removed
     */
    void removeProperty(const std::string& propName);

    /**
     * clear all of the properties
     */
    void clearProperties();

    /**
     * Returns all names of properties
     * @return all names of properties
     */
    std::vector<std::string> getPropertyNames();

    /**
     * Returns all of the properties in PropertyMap
     * @return all of the properties in PropertyMap
     */      
    std::vector<GenericData*> getProperties();

    /**
     * Returns property 
     * @param propName name of property
     * @return a pointer point to property with propName. If no property named propName
     * exists, return NULL
     */      
    GenericData* getPropertyByName(const std::string& propName);

  protected:
        
    ShortRangeInteraction();         
    ShortRangeInteraction(const ShortRangeInteraction& sri);
    ShortRangeInteraction& operator=(const ShortRangeInteraction& sri);

    SnapshotManager* snapshotMan_;
    std::vector<Atom*> atoms_;

    int globalIndex_;
    int localIndex_;
        
  private:
    
    PropertyMap properties_;
  };

}//end namespace OpenMD
#endif //PRIMITIVES_STUNTDOUBLE_HPP
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 5 months ago) by gezelter
File size:	6568 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	Content
1	/*
2	* Copyright (c) 2013 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 PRIMITIVES_SHORTRANGEINTERACTION_HPP
44	#define PRIMITIVES_SHORTRANGEINTERACTION_HPP
45
46	#include <vector>
47
48	#include "visitors/BaseVisitor.hpp"
49	#include "utils/PropertyMap.hpp"
50	#include "brains/Snapshot.hpp"
51	#include "brains/SnapshotManager.hpp"
52
53	namespace OpenMD{
54
55	/**
56	* @class ShortRangeInteraction
57	* @brief
58	*
59	* A ShortRangeInteraction holds some bookeeping data for bonded
60	* interactions (e.g. Bonds, Bends, Torsions, Inversions).
61	*
62	*/
63	class ShortRangeInteraction{
64	public:
65
66	virtual ~ShortRangeInteraction();
67
68	/**
69	* Returns the global index of this ShortRangeInteraction.
70	* @return the global index of this ShortRangeInteraction
71	*/
72	int getGlobalIndex() {
73	return globalIndex_;
74	}
75
76	/**
77	* Sets the global index of this ShortRangeInteraction.
78	* @param index new global index to be set
79	*/
80	void setGlobalIndex(int index) {
81	globalIndex_ = index;
82	}
83
84	/**
85	* Returns the local index of this ShortRangeInteraction
86	* @return the local index of this ShortRangeInteraction
87	*/
88	int getLocalIndex() {
89	return localIndex_;
90	}
91
92	/**
93	* Sets the local index of this ShortRangeInteraction
94	* @param index new index to be set
95	*/
96	void setLocalIndex(int index) {
97	localIndex_ = index;
98	}
99
100
101	/**
102	* Sets the Snapshot Manager of this ShortRangeInteraction
103	*/
104	void setSnapshotManager(SnapshotManager* sman) {
105	snapshotMan_ = sman;
106	}
107
108
109	/** Returns the name of this ShortRangeInteraction */
110	virtual std::string getName() = 0;
111
112	/** Sets the name of this ShortRangeInteraction*/
113	virtual void setName(const std::string& name) {}
114
115	/**
116	* <p>
117	* The purpose of the Visitor Pattern is to encapsulate an
118	* operation that you want to perform on the elements of a data
119	* structure. In this way, you can change the operation being
120	* performed on a structure without the need of changing the
121	* classes of the elements that you are operating on. Using a
122	* Visitor pattern allows you to decouple the classes for the data
123	* structure and the algorithms used upon them
124	* </p>
125	* @param v visitor
126	*/
127	virtual void accept(BaseVisitor* v) = 0;
128
129	/**
130	* Returns the previous value of this ShortRangeInteraction
131	* @return the value of this ShortRangeInteraction
132	*/
133	virtual RealType getPrevValue();
134
135	/**
136	* Returns the current value of this ShortRangeInteraction
137	* @return the current value of this ShortRangeInteraction
138	*/
139	virtual RealType getValue();
140
141	/**
142	* Returns the value of this ShortRangeInteraction in specified snapshot
143	* @return the value of this ShortRangeInteraction
144	* @param snapshotNo
145	*/
146	virtual RealType getValue(int snapshotNo) = 0;
147
148	virtual std::vector<Atom*> getAtoms() { return atoms_; }
149
150	/**
151	* Adds property into property map
152	* @param genData GenericData to be added into PropertyMap
153	*/
154	void addProperty(GenericData* genData);
155
156	/**
157	* Removes property from PropertyMap by name
158	* @param propName the name of property to be removed
159	*/
160	void removeProperty(const std::string& propName);
161
162	/**
163	* clear all of the properties
164	*/
165	void clearProperties();
166
167	/**
168	* Returns all names of properties
169	* @return all names of properties
170	*/
171	std::vector<std::string> getPropertyNames();
172
173	/**
174	* Returns all of the properties in PropertyMap
175	* @return all of the properties in PropertyMap
176	*/
177	std::vector<GenericData*> getProperties();
178
179	/**
180	* Returns property
181	* @param propName name of property
182	* @return a pointer point to property with propName. If no property named propName
183	* exists, return NULL
184	*/
185	GenericData* getPropertyByName(const std::string& propName);
186
187	protected:
188
189	ShortRangeInteraction();
190	ShortRangeInteraction(const ShortRangeInteraction& sri);
191	ShortRangeInteraction& operator=(const ShortRangeInteraction& sri);
192
193	SnapshotManager* snapshotMan_;
194	std::vector<Atom*> atoms_;
195
196	int globalIndex_;
197	int localIndex_;
198
199	private:
200
201	PropertyMap properties_;
202	};
203
204	}//end namespace OpenMD
205	#endif //PRIMITIVES_STUNTDOUBLE_HPP