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Comparing:
trunk/src/brains/DataStorage.hpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/DataStorage.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

# 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 53 | Line 54
54   #include <math/Vector3.hpp>
55   #include <math/SquareMatrix3.hpp>
56  
57 < namespace oopse {
57 > namespace OpenMD {
58    /**
59     * @class DataStorage
60     * @warning do not try to insert element into (or ease element from) private member data
61     * of DataStorage directly.
62 <   * @todo DataStorage may need refactorying. Every std::vector can inherit from the same base class
62 >   * @todo DataStorage may need refactoring. Every vector can inherit from the same base class
63     * which will make it easy to maintain
64     */
65    class DataStorage {
# Line 72 | Line 73 | namespace oopse {
73        dslElectroFrame = 16,
74        dslZAngle = 32,
75        dslForce = 64,
76 <      dslTorque = 128
76 >      dslTorque = 128,
77 >      dslParticlePot = 256,
78 >      dslDensity = 512,
79 >      dslFunctional = 1024,
80 >      dslFunctionalDerivative = 2048,
81 >      dslElectricField = 4096,
82 >      dslSkippedCharge = 8192
83      };
84  
78 –
85      DataStorage();
86 <    DataStorage(int size, int storageLayout = 255);
86 >    DataStorage(int size, int storageLayout = 16383);
87      /** return the size of this DataStorage. */
88      int getSize();
89      /**
# Line 86 | Line 92 | namespace oopse {
92       */
93      void resize(int newSize);
94      /**
95 <     * Reallocates memory manually. The main reason for using reserve() is efficiency
96 <     * if you know the capacity to which your std::vector must eventually grow, then it is usually more
97 <     * efficient to allocate that memory all at once.
95 >     * Reallocates memory manually.
96 >     *
97 >     * The main reason for using reserve() is efficiency if you know
98 >     * the capacity to which your vector must eventually grow,
99 >     * then it is usually more efficient to allocate that memory all
100 >     * at once.
101       */
102      void reserve(int size);
103      /**
104       * Copies data inside DataStorage class.
105 <     * Copy function actually call std::copy for every std::vector in DataStorage class.
106 <     * One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
105 >     *
106 >     * Copy function actually call copy for every vector in
107 >     * DataStorage class.  One Precondition of copy is that
108 >     * target is not within the range [source, soruce + num]
109 >     *
110       * @param souce
111       * @param num number of element to be moved
112       * @param target
# Line 107 | Line 119 | namespace oopse {
119      /** Returns the pointer of internal array */
120      RealType *getArrayPointer(int whichArray);
121  
122 <    std::vector<Vector3d> position;               /** position array */
123 <    std::vector<Vector3d> velocity;               /** velocity array */
124 <    std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
125 <    std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
126 <    std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
127 <    std::vector<RealType> zAngle;              /** z -angle array */        
128 <    std::vector<Vector3d> force;               /** force array */
129 <    std::vector<Vector3d> torque;               /** torque array */
122 >    std::vector<Vector3d> position;        /** position array */
123 >    std::vector<Vector3d> velocity;        /** velocity array */
124 >    std::vector<RotMat3x3d> aMat;          /** rotation matrix array */
125 >    std::vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
126 >    std::vector<Mat3x3d> electroFrame;     /** the lab frame unit std::vector array*/
127 >    std::vector<RealType> zAngle;          /** z-angle array */        
128 >    std::vector<Vector3d> force;           /** force array */
129 >    std::vector<Vector3d> torque;          /** torque array */
130 >    std::vector<RealType> particlePot;     /** particle potential arrray */
131 >    std::vector<RealType> density;         /** electron density */
132 >    std::vector<RealType> functional;      /** density functional */
133 >    std::vector<RealType> functionalDerivative; /** derivative of functional */
134 >    std::vector<Vector3d> electricField;   /** local electric field */
135 >    std::vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
136  
137      static int getBytesPerStuntDouble(int layout);
138  
139    private:
140  
141 <    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
124 <            
141 >    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);            
142      RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
143      RealType* internalGetArrayPointer(std::vector<RealType>& v);
144 +
145              
146      template<typename T>
147      void internalResize(std::vector<T>& v, int newSize);

Comparing:
trunk/src/brains/DataStorage.hpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/DataStorage.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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