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, 5 months ago) by gezelter
Original Path:	*trunk/src/brains/DataStorage.hpp*
File size:	5379 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	tim	155	*
4	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	tim	155	*/
41	gezelter	246
42	tim	155	/**
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	gezelter	1390	namespace OpenMD {
57	gezelter	507	/**
58			* @class DataStorage
59			* @warning do not try to insert element into (or ease element from) private member data
60			* of DataStorage directly.
61	gezelter	1104	* @todo DataStorage may need refactoring. Every std::vector can inherit from the same base class
62	gezelter	507	* which will make it easy to maintain
63			*/
64			class DataStorage {
65			public:
66	tim	155
67	gezelter	507	enum{
68			dslPosition = 1,
69			dslVelocity = 2,
70			dslAmat = 4,
71			dslAngularMomentum = 8,
72			dslElectroFrame = 16,
73			dslZAngle = 32,
74			dslForce = 64,
75	chuckv	1245	dslTorque = 128,
76			dslParticlePot = 256
77	gezelter	507	};
78	tim	155
79
80	gezelter	507	DataStorage();
81	chuckv	1245	DataStorage(int size, int storageLayout = 511);
82	gezelter	507	/** 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	tim	963	RealType *getArrayPointer(int whichArray);
110	gezelter	246
111	gezelter	507	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	tim	963	std::vector<RealType> zAngle; /** z -angle array */
117	gezelter	507	std::vector<Vector3d> force; /** force array */
118			std::vector<Vector3d> torque; /** torque array */
119	chuckv	1245	std::vector<RealType> particlePot; /** pair potential arrray */
120	gezelter	246
121	gezelter	507	static int getBytesPerStuntDouble(int layout);
122	tim	323
123	gezelter	507	private:
124	tim	155
125	tim	963	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
126	tim	155
127	tim	963	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
128			RealType* internalGetArrayPointer(std::vector<RealType>& v);
129	gezelter	1104
130	tim	155
131	gezelter	507	template<typename T>
132			void internalResize(std::vector<T>& v, int newSize);
133	tim	155
134	gezelter	507	template<typename T>
135			void internalCopy(std::vector<T>& v, int source, int num, int target);
136	tim	155
137	gezelter	507	int size_;
138			int storageLayout_;
139	gezelter	246
140	gezelter	507	};
141	tim	155
142	tim	323	}
143	tim	155	#endif //BRAINS_DATASTORAGE_HPP