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Comparing trunk/src/brains/DataStorage.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  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 {
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 refactorying. Every std::vector can inherit from the same base class
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 {
# Line 72 | Line 72 | namespace oopse {
72        dslElectroFrame = 16,
73        dslZAngle = 32,
74        dslForce = 64,
75 <      dslTorque = 128
75 >      dslTorque = 128,
76 >      dslParticlePot = 256
77      };
78  
79  
80      DataStorage();
81 <    DataStorage(int size, int storageLayout = 255);
81 >    DataStorage(int size, int storageLayout = 511);
82      /** return the size of this DataStorage. */
83      int getSize();
84      /**
# Line 105 | Line 106 | namespace oopse {
106      /** Sets the storage layout  */
107      void setStorageLayout(int layout);
108      /** Returns the pointer of internal array */
109 <    double *getArrayPointer(int whichArray);
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 */        
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);
122  
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);

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