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root/OpenMD/branches/development/src/brains/DataStorage.hpp

Comparing:
trunk/src/brains/DataStorage.hpp (file contents), Revision 189 by tim, Thu Oct 28 22:34:01 2004 UTC vs.
branches/development/src/brains/DataStorage.hpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 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. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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	<
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 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 refactoring. 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	+	dslParticlePot = 256,
77	+	dslDensity = 512,
78	+	dslFunctional = 1024,
79	+	dslFunctionalDerivative = 2048,
80	+	dslElectricField = 4096
81	+	};
82
83
84	<	//forward declaration
85	<	class Snapshot;
86	<	class StuntDouble;
87	<	class DataStorageTestCase;
84	>	DataStorage();
85	>	DataStorage(int size, int storageLayout = 8191);
86	>	/** return the size of this DataStorage. */
87	>	int getSize();
88		/**
89	<	* @class DataStorage
90	<	* @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
89	>	* Changes the size of this DataStorage.
90	>	* @param size new size of this DataStorage
91		*/
92	<	class DataStorage {
93	<	public:
92	>	void resize(int newSize);
93	>	/**
94	>	* Reallocates memory manually.
95	>	*
96	>	* The main reason for using reserve() is efficiency if you know
97	>	* the capacity to which your std::vector must eventually grow,
98	>	* then it is usually more efficient to allocate that memory all
99	>	* at once.
100	>	*/
101	>	void reserve(int size);
102	>	/**
103	>	* Copies data inside DataStorage class.
104	>	*
105	>	* Copy function actually call std::copy for every std::vector in
106	>	* DataStorage class.  One Precondition of std::copy is that
107	>	* target is not within the range [soruce, soruce + num]
108	>	*
109	>	* @param souce
110	>	* @param num number of element to be moved
111	>	* @param target
112	>	*/
113	>	void copy(int source, int num, int target);
114	>	/** Returns the storage layout  */
115	>	int getStorageLayout();
116	>	/** Sets the storage layout  */
117	>	void setStorageLayout(int layout);
118	>	/** Returns the pointer of internal array */
119	>	RealType *getArrayPointer(int whichArray);
120
121	<	enum{
122	<	dslPosition = 1,
123	<	dslVelocity = 2,
124	<	dslAmat = 4,
125	<	dslAngularMomentum = 8,
126	<	dslUnitVector = 16,
127	<	dslZAngle = 32,
128	<	dslForce = 64,
129	<	dslTorque = 128
130	<	};
121	>	std::vector<Vector3d> position;        /** position array */
122	>	std::vector<Vector3d> velocity;        /** velocity array */
123	>	std::vector<RotMat3x3d> aMat;          /** rotation matrix array */
124	>	std::vector<Vector3d> angularMomentum; /** angular momentum array
125	>	(body-fixed) */
126	>	std::vector<Mat3x3d> electroFrame;     /** the lab frame unit 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
136	+	static int getBytesPerStuntDouble(int layout);
137
138	<	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:
138	>	private:
139
140	+	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
141	+	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
142	+	RealType* internalGetArrayPointer(std::vector<RealType>& v);
143
105	–	double* internalGetArrayPointer(std::vector<Vector3d>& v);
144
145	<	double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
146	<	double* internalGetArrayPointer(std::vector<double>& v);
109	<
110	<	template<typename T>
111	<	void internalResize(std::vector<T>& v, int newSize);
145	>	template<typename T>
146	>	void internalResize(std::vector<T>& v, int newSize);
147
148	<	template<typename T>
149	<	void interalCopy(std::vector<T>& v, int source,  int num, int target);
148	>	template<typename T>
149	>	void internalCopy(std::vector<T>& v, int source,  int num, int target);
150
151	<	int size_;
152	<	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	<	};
151	>	int size_;
152	>	int storageLayout_;
153
154	+	};
155
156	+	}
157		#endif //BRAINS_DATASTORAGE_HPP

Comparing:
trunk/src/brains/DataStorage.hpp (property svn:keywords), Revision 189 by tim, Thu Oct 28 22:34:01 2004 UTC vs.
branches/development/src/brains/DataStorage.hpp (property svn:keywords), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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