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root/OpenMD/trunk/src/brains/DataStorage.hpp
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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 246 by gezelter, Wed Jan 12 22:41:40 2005 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.
1 > /*
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 39 | Line 55 | using namespace oopse;
55  
56   using namespace oopse;
57  
42 –
43 –
44 –    //forward declaration
45 –    class Snapshot;
46 –    class StuntDouble;
47 –    class DataStorageTestCase;
58      /**
59       * @class DataStorage
60       * @warning do not try to insert element into (or ease element from) private member data
# Line 60 | Line 70 | using namespace oopse;
70                  dslVelocity = 2,
71                  dslAmat = 4,
72                  dslAngularMomentum = 8,
73 <                dslUnitVector = 16,
73 >                dslElectroFrame = 16,
74                  dslZAngle = 32,
75                  dslForce = 64,
76                  dslTorque = 128
# Line 68 | Line 78 | using namespace oopse;
78  
79  
80              DataStorage();
81 <            DataStorage(int size, int storageLayout = 0x11111111);
81 >            DataStorage(int size, int storageLayout = 255);
82              /** return the size of this DataStorage. */
83              int getSize();
84              /**
# Line 97 | Line 107 | using namespace oopse;
107              void setStorageLayout(int layout);
108              /** Returns the pointer of internal array */
109              double *getArrayPointer(int whichArray);
100 –            friend class StuntDouble;
101 –            friend class DataStorageTestCase;
102 –        private:
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 */
119  
120 +        private:
121 +
122              double* internalGetArrayPointer(std::vector<Vector3d>& v);
123              
124              double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
# Line 111 | Line 128 | using namespace oopse;
128              void internalResize(std::vector<T>& v, int newSize);
129  
130              template<typename T>
131 <            void interalCopy(std::vector<T>& v, int source,  int num, int target);
131 >            void internalCopy(std::vector<T>& v, int source,  int num, int target);
132              
133              int size_;
134              int storageLayout_;
135 <            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 */
135 >
136      };
137  
138  

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