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Comparing trunk/src/brains/DataStorage.hpp (file contents):
Revision 189 by tim, Thu Oct 28 22:34:01 2004 UTC vs.
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC

# Line 1 | Line 1
1   /*
2 < * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3 < *
4 < * Contact: oopse@oopse.org
5 < *
6 < * This program is free software; you can redistribute it and/or
7 < * modify it under the terms of the GNU Lesser General Public License
8 < * as published by the Free Software Foundation; either version 2.1
9 < * of the License, or (at your option) any later version.
10 < * All we ask is that proper credit is given for our work, which includes
11 < * - but is not limited to - adding the above copyright notice to the beginning
12 < * of your source code files, and to any copyright notice that you may distribute
13 < * with programs based on this work.
14 < *
15 < * This program is distributed in the hope that it will be useful,
16 < * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 < * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 < * GNU Lesser General Public License for more details.
19 < *
20 < * You should have received a copy of the GNU Lesser General Public License
21 < * along with this program; if not, write to the Free Software
22 < * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
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. 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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40   */
41 <
41 >
42   /**
43   * @file Vector.hpp
44   * @author Teng Lin
# Line 37 | Line 53
53   #include <math/Vector3.hpp>
54   #include <math/SquareMatrix3.hpp>
55  
56 < using namespace oopse;
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:
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 +    };
77  
78  
79 <    //forward declaration
80 <    class Snapshot;
81 <    class StuntDouble;
82 <    class DataStorageTestCase;
79 >    DataStorage();
80 >    DataStorage(int size, int storageLayout = 255);
81 >    /** return the size of this DataStorage. */
82 >    int getSize();
83      /**
84 <     * @class DataStorage
85 <     * @warning do not try to insert element into (or ease element from) private member data
51 <     * of DataStorage directly.
52 <     * @todo DataStorage may need refactorying. Every std::vector can inherit from the same base class
53 <     * which will make it easy to maintain
84 >     * Changes the size of this DataStorage.
85 >     * @param size new size of this DataStorage
86       */
87 <    class DataStorage {
88 <        public:
87 >    void resize(int newSize);
88 >    /**
89 >     * Reallocates memory manually. The main reason for using reserve() is efficiency
90 >     * if you know the capacity to which your std::vector must eventually grow, then it is usually more
91 >     * efficient to allocate that memory all at once.
92 >     */
93 >    void reserve(int size);
94 >    /**
95 >     * Copies data inside DataStorage class.
96 >     * Copy function actually call std::copy for every std::vector in DataStorage class.
97 >     * One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
98 >     * @param souce
99 >     * @param num number of element to be moved
100 >     * @param target
101 >     */
102 >    void copy(int source, int num, int target);
103 >    /** Returns the storage layout  */
104 >    int getStorageLayout();
105 >    /** Sets the storage layout  */
106 >    void setStorageLayout(int layout);
107 >    /** Returns the pointer of internal array */
108 >    RealType *getArrayPointer(int whichArray);
109  
110 <            enum{
111 <                dslPosition = 1,
112 <                dslVelocity = 2,
113 <                dslAmat = 4,
114 <                dslAngularMomentum = 8,
115 <                dslUnitVector = 16,
116 <                dslZAngle = 32,
117 <                dslForce = 64,
66 <                dslTorque = 128
67 <            };
110 >    std::vector<Vector3d> position;               /** position array */
111 >    std::vector<Vector3d> velocity;               /** velocity array */
112 >    std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
113 >    std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
114 >    std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
115 >    std::vector<RealType> zAngle;              /** z -angle array */        
116 >    std::vector<Vector3d> force;               /** force array */
117 >    std::vector<Vector3d> torque;               /** torque array */
118  
119 +    static int getBytesPerStuntDouble(int layout);
120  
121 <            DataStorage();
71 <            DataStorage(int size, int storageLayout = 0x11111111);
72 <            /** return the size of this DataStorage. */
73 <            int getSize();
74 <            /**
75 <             * Changes the size of this DataStorage.
76 <             * @param size new size of this DataStorage
77 <             */
78 <            void resize(int newSize);
79 <            /**
80 <             * Reallocates memory manually. The main reason for using reserve() is efficiency
81 <             * if you know the capacity to which your std::vector must eventually grow, then it is usually more
82 <             * efficient to allocate that memory all at once.
83 <             */
84 <            void reserve(int size);
85 <            /**
86 <             * Copies data inside DataStorage class.
87 <             * Copy function actually call std::copy for every std::vector in DataStorage class.
88 <             * One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
89 <             * @param souce
90 <             * @param num number of element to be moved
91 <             * @param target
92 <             */
93 <            void copy(int source, int num, int target);
94 <            /** Returns the storage layout  */
95 <            int getStorageLayout();
96 <            /** Sets the storage layout  */
97 <            void setStorageLayout(int layout);
98 <            /** Returns the pointer of internal array */
99 <            double *getArrayPointer(int whichArray);
100 <            friend class StuntDouble;
101 <            friend class DataStorageTestCase;
102 <        private:
121 >  private:
122  
123 <
105 <            double* internalGetArrayPointer(std::vector<Vector3d>& v);
123 >    RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
124              
125 <            double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
126 <            double* internalGetArrayPointer(std::vector<double>& v);
125 >    RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
126 >    RealType* internalGetArrayPointer(std::vector<RealType>& v);
127              
128 <            template<typename T>
129 <            void internalResize(std::vector<T>& v, int newSize);
128 >    template<typename T>
129 >    void internalResize(std::vector<T>& v, int newSize);
130  
131 <            template<typename T>
132 <            void interalCopy(std::vector<T>& v, int source,  int num, int target);
131 >    template<typename T>
132 >    void internalCopy(std::vector<T>& v, int source,  int num, int target);
133              
134 <            int size_;
135 <            int storageLayout_;
118 <            std::vector<Vector3d> position;               /** position array */
119 <            std::vector<Vector3d> velocity;               /** velocity array */
120 <            std::vector<RotMat3x3d> aMat;            /** rotation matrix array */
121 <            std::vector<Vector3d> angularMomentum;/** angular momentum array (body-fixed) */
122 <            std::vector<Vector3d> unitVector;                /** the lab frame unit std::vector array*/
123 <            std::vector<double> zAngle;              /** z -angle array */        
124 <            std::vector<Vector3d> force;               /** force array */
125 <            std::vector<Vector3d> torque;               /** torque array */
126 <    };
134 >    int size_;
135 >    int storageLayout_;
136  
137 +  };
138  
139 + }
140   #endif //BRAINS_DATASTORAGE_HPP

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