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Comparing trunk/src/brains/DataStorage.hpp (file contents):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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   /**
# Line 53 | Line 53
53   #include <math/Vector3.hpp>
54   #include <math/SquareMatrix3.hpp>
55  
56 < namespace oopse {
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 refactorying. Every std::vector can inherit from the same base class
62 <     * which will make it easy to maintain
63 <     */
64 <    class DataStorage {
65 <        public:
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 <            };
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 = 255);
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 <            double *getArrayPointer(int whichArray);
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<double> zAngle;              /** z -angle array */        
117 <            std::vector<Vector3d> force;               /** force array */
118 <            std::vector<Vector3d> torque;               /** torque array */
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);
121 >    static int getBytesPerStuntDouble(int layout);
122  
123 <        private:
123 >  private:
124  
125 <            double* internalGetArrayPointer(std::vector<Vector3d>& v);
125 >    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
126              
127 <            double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
128 <            double* internalGetArrayPointer(std::vector<double>& v);
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);
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);
134 >    template<typename T>
135 >    void internalCopy(std::vector<T>& v, int source,  int num, int target);
136              
137 <            int size_;
138 <            int storageLayout_;
137 >    int size_;
138 >    int storageLayout_;
139  
140 <    };
140 >  };
141  
142   }
143   #endif //BRAINS_DATASTORAGE_HPP

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