src/brains/DataStorage.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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file Vector.hpp
 * @author Teng Lin
 * @date 09/14/2004
 * @version 1.0
 */

#ifndef BRAINS_DATASTORAGE_HPP
#define BRAINS_DATASTORAGE_HPP

#include <vector>
#include <math/Vector3.hpp>
#include <math/SquareMatrix3.hpp>

namespace OpenMD {
  /**
   * @class DataStorage
   * @warning do not try to insert element into (or ease element from) private member data 
   * of DataStorage directly.
   * @todo DataStorage may need refactoring. Every std::vector can inherit from the same base class
   * which will make it easy to maintain
   */
  class DataStorage {
  public:

    enum{
      dslPosition = 1,
      dslVelocity = 2,
      dslAmat = 4, 
      dslAngularMomentum = 8,
      dslElectroFrame = 16,
      dslZAngle = 32,
      dslForce = 64, 
      dslTorque = 128,
      dslParticlePot = 256
    };


    DataStorage();
    DataStorage(int size, int storageLayout = 511);
    /** return the size of this DataStorage. */
    int getSize();
    /**
     * Changes the size of this DataStorage.
     * @param size new size of this DataStorage
     */
    void resize(int newSize);
    /**
     * Reallocates memory manually. The main reason for using reserve() is efficiency
     * if you know the capacity to which your std::vector must eventually grow, then it is usually more
     * efficient to allocate that memory all at once.
     */
    void reserve(int size);
    /**
     * Copies data inside DataStorage class.
     * Copy function actually call std::copy for every std::vector in DataStorage class. 
     * One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
     * @param souce 
     * @param num number of element to be moved
     * @param target
     */
    void copy(int source, int num, int target);
    /** Returns the storage layout  */
    int getStorageLayout();
    /** Sets the storage layout  */
    void setStorageLayout(int layout);
    /** Returns the pointer of internal array */
    RealType *getArrayPointer(int whichArray);

    std::vector<Vector3d> position;               /** position array */
    std::vector<Vector3d> velocity;               /** velocity array */
    std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
    std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
    std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
    std::vector<RealType> zAngle;              /** z -angle array */        
    std::vector<Vector3d> force;               /** force array */
    std::vector<Vector3d> torque;               /** torque array */
    std::vector<RealType> particlePot;         /** pair potential arrray */

    static int getBytesPerStuntDouble(int layout);

  private:

    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
            
    RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
    RealType* internalGetArrayPointer(std::vector<RealType>& v);

            
    template<typename T>
    void internalResize(std::vector<T>& v, int newSize);

    template<typename T>
    void internalCopy(std::vector<T>& v, int source,  int num, int target);
            
    int size_;
    int storageLayout_;

  };

}
#endif //BRAINS_DATASTORAGE_HPP
Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 11 months ago) by gezelter
File size:	5379 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	/**
43	* @file Vector.hpp
44	* @author Teng Lin
45	* @date 09/14/2004
46	* @version 1.0
47	*/
48
49	#ifndef BRAINS_DATASTORAGE_HPP
50	#define BRAINS_DATASTORAGE_HPP
51
52	#include <vector>
53	#include <math/Vector3.hpp>
54	#include <math/SquareMatrix3.hpp>
55
56	namespace OpenMD {
57	/**
58	* @class DataStorage
59	* @warning do not try to insert element into (or ease element from) private member data
60	* of DataStorage directly.
61	* @todo DataStorage may need refactoring. Every std::vector can inherit from the same base class
62	* which will make it easy to maintain
63	*/
64	class DataStorage {
65	public:
66
67	enum{
68	dslPosition = 1,
69	dslVelocity = 2,
70	dslAmat = 4,
71	dslAngularMomentum = 8,
72	dslElectroFrame = 16,
73	dslZAngle = 32,
74	dslForce = 64,
75	dslTorque = 128,
76	dslParticlePot = 256
77	};
78
79
80	DataStorage();
81	DataStorage(int size, int storageLayout = 511);
82	/** return the size of this DataStorage. */
83	int getSize();
84	/**
85	* Changes the size of this DataStorage.
86	* @param size new size of this DataStorage
87	*/
88	void resize(int newSize);
89	/**
90	* Reallocates memory manually. The main reason for using reserve() is efficiency
91	* if you know the capacity to which your std::vector must eventually grow, then it is usually more
92	* efficient to allocate that memory all at once.
93	*/
94	void reserve(int size);
95	/**
96	* Copies data inside DataStorage class.
97	* Copy function actually call std::copy for every std::vector in DataStorage class.
98	* One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
99	* @param souce
100	* @param num number of element to be moved
101	* @param target
102	*/
103	void copy(int source, int num, int target);
104	/** Returns the storage layout */
105	int getStorageLayout();
106	/** Sets the storage layout */
107	void setStorageLayout(int layout);
108	/** Returns the pointer of internal array */
109	RealType *getArrayPointer(int whichArray);
110
111	std::vector<Vector3d> position; /** position array */
112	std::vector<Vector3d> velocity; /** velocity array */
113	std::vector<RotMat3x3d> aMat; /** rotation matrix array */
114	std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
115	std::vector<Mat3x3d> electroFrame; /** the lab frame unit std::vector array*/
116	std::vector<RealType> zAngle; /** z -angle array */
117	std::vector<Vector3d> force; /** force array */
118	std::vector<Vector3d> torque; /** torque array */
119	std::vector<RealType> particlePot; /** pair potential arrray */
120
121	static int getBytesPerStuntDouble(int layout);
122
123	private:
124
125	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
126
127	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
128	RealType* internalGetArrayPointer(std::vector<RealType>& v);
129
130
131	template<typename T>
132	void internalResize(std::vector<T>& v, int newSize);
133
134	template<typename T>
135	void internalCopy(std::vector<T>& v, int source, int num, int target);
136
137	int size_;
138	int storageLayout_;
139
140	};
141
142	}
143	#endif //BRAINS_DATASTORAGE_HPP