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 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,
      dslDensity = 512,
      dslFunctional = 1024,
      dslFunctionalDerivative = 2048,
      dslElectricField = 4096,
      dslSkippedCharge = 8192
    };

    DataStorage();
    DataStorage(int size, int storageLayout = 16383);
    /** 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 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 copy for every vector in
     * DataStorage class.  One Precondition of copy is that
     * target is not within the range [source, 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;     /** particle potential arrray */
    std::vector<RealType> density;         /** electron density */
    std::vector<RealType> functional;      /** density functional */
    std::vector<RealType> functionalDerivative; /** derivative of functional */
    std::vector<Vector3d> electricField;   /** local electric field */
    std::vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */

    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:	1584
Committed:	Fri Jun 17 20:16:35 2011 UTC (13 years, 10 months ago) by gezelter
File size:	5896 byte(s)
Log Message:	bug fixes.
#	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 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	dslDensity = 512,
78	dslFunctional = 1024,
79	dslFunctionalDerivative = 2048,
80	dslElectricField = 4096,
81	dslSkippedCharge = 8192
82	};
83
84	DataStorage();
85	DataStorage(int size, int storageLayout = 16383);
86	/** return the size of this DataStorage. */
87	int getSize();
88	/**
89	* Changes the size of this DataStorage.
90	* @param size new size of this DataStorage
91	*/
92	void resize(int newSize);
93	/**
94	* Reallocates memory manually.
95	*
96	* The main reason for using reserve() is efficiency if you know
97	* the capacity to which your vector must eventually grow,
98	* then it is usually more efficient to allocate that memory all
99	* at once.
100	*/
101	void reserve(int size);
102	/**
103	* Copies data inside DataStorage class.
104	*
105	* Copy function actually call copy for every vector in
106	* DataStorage class. One Precondition of copy is that
107	* target is not within the range [source, soruce + num]
108	*
109	* @param souce
110	* @param num number of element to be moved
111	* @param target
112	*/
113	void copy(int source, int num, int target);
114	/** Returns the storage layout */
115	int getStorageLayout();
116	/** Sets the storage layout */
117	void setStorageLayout(int layout);
118	/** Returns the pointer of internal array */
119	RealType *getArrayPointer(int whichArray);
120
121	std::vector<Vector3d> position; /** position array */
122	std::vector<Vector3d> velocity; /** velocity array */
123	std::vector<RotMat3x3d> aMat; /** rotation matrix array */
124	std::vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
125	std::vector<Mat3x3d> electroFrame; /** the lab frame unit std::vector array*/
126	std::vector<RealType> zAngle; /** z-angle array */
127	std::vector<Vector3d> force; /** force array */
128	std::vector<Vector3d> torque; /** torque array */
129	std::vector<RealType> particlePot; /** particle potential arrray */
130	std::vector<RealType> density; /** electron density */
131	std::vector<RealType> functional; /** density functional */
132	std::vector<RealType> functionalDerivative; /** derivative of functional */
133	std::vector<Vector3d> electricField; /** local electric field */
134	std::vector<RealType> skippedCharge; /** charge skipped during normal pairwise calculation */
135
136	static int getBytesPerStuntDouble(int layout);
137
138	private:
139
140	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
141	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
142	RealType* internalGetArrayPointer(std::vector<RealType>& v);
143
144
145	template<typename T>
146	void internalResize(std::vector<T>& v, int newSize);
147
148	template<typename T>
149	void internalCopy(std::vector<T>& v, int source, int num, int target);
150
151	int size_;
152	int storageLayout_;
153
154	};
155
156	}
157	#endif //BRAINS_DATASTORAGE_HPP