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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.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 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 > using namespace std;
58 > namespace OpenMD {
59    /**
60     * @class DataStorage
61     * @warning do not try to insert element into (or ease element from) private member data
62     * of DataStorage directly.
63 <   * @todo DataStorage may need refactorying. Every std::vector can inherit from the same base class
63 >   * @todo DataStorage may need refactoring. Every vector can inherit from the same base class
64     * which will make it easy to maintain
65     */
66    class DataStorage {
# Line 70 | Line 72 | namespace oopse {
72        dslAmat = 4,
73        dslAngularMomentum = 8,
74        dslElectroFrame = 16,
75 <      dslZAngle = 32,
76 <      dslForce = 64,
77 <      dslTorque = 128
75 >      dslForce = 32,
76 >      dslTorque = 64,
77 >      dslParticlePot = 128,
78 >      dslDensity = 256,
79 >      dslFunctional = 512,
80 >      dslFunctionalDerivative = 1024,
81 >      dslElectricField = 2048,
82 >      dslSkippedCharge = 4096,
83 >      dslFlucQPosition = 8192,
84 >      dslFlucQVelocity = 16384,
85 >      dslFlucQForce = 32768
86      };
87  
78 –
88      DataStorage();
89 <    DataStorage(int size, int storageLayout = 255);
89 >    DataStorage(int size, int storageLayout = 0);
90      /** return the size of this DataStorage. */
91      int getSize();
92      /**
# Line 86 | Line 95 | namespace oopse {
95       */
96      void resize(int newSize);
97      /**
98 <     * Reallocates memory manually. The main reason for using reserve() is efficiency
99 <     * if you know the capacity to which your std::vector must eventually grow, then it is usually more
100 <     * efficient to allocate that memory all at once.
98 >     * Reallocates memory manually.
99 >     *
100 >     * The main reason for using reserve() is efficiency if you know
101 >     * the capacity to which your vector must eventually grow,
102 >     * then it is usually more efficient to allocate that memory all
103 >     * at once.
104       */
105      void reserve(int size);
106      /**
107       * Copies data inside DataStorage class.
108 <     * Copy function actually call std::copy for every std::vector in DataStorage class.
109 <     * One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
110 <     * @param souce
108 >     *
109 >     * Copy function actually calls copy for every vector in
110 >     * DataStorage class.  One Precondition of copy is that
111 >     * target is not within the range [source, soruce + num]
112 >     *
113 >     * @param source
114       * @param num number of element to be moved
115       * @param target
116       */
# Line 107 | Line 122 | namespace oopse {
122      /** Returns the pointer of internal array */
123      RealType *getArrayPointer(int whichArray);
124  
125 <    std::vector<Vector3d> position;               /** position array */
126 <    std::vector<Vector3d> velocity;               /** velocity array */
127 <    std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
128 <    std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
129 <    std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
130 <    std::vector<RealType> zAngle;              /** z -angle array */        
131 <    std::vector<Vector3d> force;               /** force array */
132 <    std::vector<Vector3d> torque;               /** torque array */
125 >    vector<Vector3d> position;        /** position array */
126 >    vector<Vector3d> velocity;        /** velocity array */
127 >    vector<RotMat3x3d> aMat;          /** rotation matrix array */
128 >    vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
129 >    vector<Mat3x3d> electroFrame;     /** the lab frame unit vector array*/
130 >    vector<Vector3d> force;           /** force array */
131 >    vector<Vector3d> torque;          /** torque array */
132 >    vector<RealType> particlePot;     /** particle potential arrray */
133 >    vector<RealType> density;         /** electron density */
134 >    vector<RealType> functional;      /** density functional */
135 >    vector<RealType> functionalDerivative; /** derivative of functional */
136 >    vector<Vector3d> electricField;   /** local electric field */
137 >    vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
138 >    vector<RealType> flucQPos;        /** fluctuating charges */
139 >    vector<RealType> flucQVel;        /** fluctuating charge velocities */
140 >    vector<RealType> flucQFrc;        /** fluctuating charge forces */
141  
142      static int getBytesPerStuntDouble(int layout);
143  
144    private:
145  
146 <    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
146 >    RealType* internalGetArrayPointer(vector<Vector3d>& v);            
147 >    RealType* internalGetArrayPointer(vector<RotMat3x3d>& v);
148 >    RealType* internalGetArrayPointer(vector<RealType>& v);
149 >
150              
125 –    RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
126 –    RealType* internalGetArrayPointer(std::vector<RealType>& v);
127 –            
151      template<typename T>
152      void internalResize(std::vector<T>& v, int newSize);
153  

Comparing trunk/src/brains/DataStorage.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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