ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/brains/DataStorage.hpp (file contents), Revision 323 by tim, Sun Feb 13 15:56:10 2005 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	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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 {
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:
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	<	};
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	<	DataStorage();
85	<	DataStorage(int size, int storageLayout = 255);
86	<	/** return the size of this DataStorage. */
87	<	int getSize();
88	<	/**
89	<	* Changes the size of this DataStorage.
90	<	* @param size new size of this DataStorage
91	<	*/
92	<	void resize(int newSize);
93	<	/**
94	<	* Reallocates memory manually. The main reason for using reserve() is efficiency
95	<	* if you know the capacity to which your std::vector must eventually grow, then it is usually more
96	<	* efficient to allocate that memory all at once.
97	<	*/
98	<	void reserve(int size);
99	<	/**
100	<	* Copies data inside DataStorage class.
101	<	* Copy function actually call std::copy for every std::vector in DataStorage class.
102	<	* One Precondition of std::copy is that target is not within the range [soruce, soruce + num]
103	<	* @param souce
104	<	* @param num number of element to be moved
105	<	* @param target
106	<	*/
107	<	void copy(int source, int num, int target);
108	<	/** Returns the storage layout  */
109	<	int getStorageLayout();
110	<	/** Sets the storage layout  */
111	<	void setStorageLayout(int layout);
112	<	/** Returns the pointer of internal array */
113	<	double *getArrayPointer(int whichArray);
84	>	DataStorage();
85	>	DataStorage(int size, int storageLayout = 8191);
86	>	/** return the size of this DataStorage. */
87	>	int getSize();
88	>	/**
89	>	* Changes the size of this DataStorage.
90	>	* @param size new size of this DataStorage
91	>	*/
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	<	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 (body-fixed) */
125	<	std::vector<Mat3x3d> electroFrame;                /** the lab frame unit std::vector array*/
126	<	std::vector<double> zAngle;              /** z -angle array */
127	<	std::vector<Vector3d> force;               /** force array */
128	<	std::vector<Vector3d> torque;               /** torque array */
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);
136	>	static int getBytesPerStuntDouble(int layout);
137
138	<	private:
138	>	private:
139
140	<	double* internalGetArrayPointer(std::vector<Vector3d>& v);
140	>	RealType* internalGetArrayPointer(std::vector<Vector3d>& v);
141	>	RealType* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
142	>	RealType* internalGetArrayPointer(std::vector<RealType>& v);
143	>
144
145	<	double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
146	<	double* internalGetArrayPointer(std::vector<double>& v);
127	<
128	<	template<typename T>
129	<	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 internalCopy(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_;
151	>	int size_;
152	>	int storageLayout_;
153
154	<	};
154	>	};
155
156		}
157		#endif //BRAINS_DATASTORAGE_HPP

Comparing:
trunk/src/brains/DataStorage.hpp (property svn:keywords), Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
branches/development/src/brains/DataStorage.hpp (property svn:keywords), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines