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Comparing trunk/src/brains/DataStorage.hpp (file contents):
Revision 323 by tim, Sun Feb 13 15:56:10 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 53 | Line 54
54		#include <math/Vector3.hpp>
55		#include <math/SquareMatrix3.hpp>
56
57	<	namespace oopse {
57	>	using namespace std;
58	>	namespace OpenMD {
59	>	/**
60	>	* @class DataStorage
61	>	* @warning do not try to insert element into (or ease element from) private member data
62	>	* of DataStorage directly.
63	>	* @todo DataStorage may need refactoring. Every vector can inherit from the same base class
64	>	* which will make it easy to maintain
65	>	*/
66	>	class DataStorage {
67	>	public:
68	>
69	>	enum{
70	>	dslPosition = 1,
71	>	dslVelocity = 2,
72	>	dslForce = 4,
73	>	dslAmat = 8,
74	>	dslAngularMomentum = 16,
75	>	dslTorque = 32,
76	>	dslParticlePot = 64,
77	>	dslDensity = 128,
78	>	dslFunctional = 256,
79	>	dslFunctionalDerivative = 512,
80	>	dslDipole = 1024,
81	>	dslQuadrupole = 2048,
82	>	dslElectricField = 4096,
83	>	dslSkippedCharge = 8192,
84	>	dslFlucQPosition = 16384,
85	>	dslFlucQVelocity = 32768,
86	>	dslFlucQForce = 65536
87	>	};
88	>
89	>	DataStorage();
90	>	DataStorage(int size, int storageLayout = 0);
91	>	/** return the size of this DataStorage. */
92	>	int getSize();
93		/**
94	<	* @class DataStorage
95	<	* @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
94	>	* Changes the size of this DataStorage.
95	>	* @param newSize new size of this DataStorage
96		*/
97	<	class DataStorage {
98	<	public:
97	>	void resize(int newSize);
98	>	/**
99	>	* Reallocates memory manually.
100	>	*
101	>	* The main reason for using reserve() is efficiency if you know
102	>	* the capacity to which your vector must eventually grow,
103	>	* then it is usually more efficient to allocate that memory all
104	>	* at once.
105	>	*/
106	>	void reserve(int size);
107	>	/**
108	>	* Copies data inside DataStorage class.
109	>	*
110	>	* Copy function actually calls copy for every vector in
111	>	* DataStorage class.  One Precondition of copy is that
112	>	* target is not within the range [source, soruce + num]
113	>	*
114	>	* @param source
115	>	* @param num number of element to be moved
116	>	* @param target
117	>	*/
118	>	void copy(int source, int num, int target);
119	>	/** Returns the storage layout  */
120	>	int getStorageLayout();
121	>	/** Sets the storage layout  */
122	>	void setStorageLayout(int layout);
123	>	/** Returns the pointer of internal array */
124	>	RealType *getArrayPointer(int whichArray);
125
126	<	enum{
127	<	dslPosition = 1,
128	<	dslVelocity = 2,
129	<	dslAmat = 4,
130	<	dslAngularMomentum = 8,
131	<	dslElectroFrame = 16,
132	<	dslZAngle = 32,
133	<	dslForce = 64,
134	<	dslTorque = 128
135	<	};
126	>	vector<Vector3d> position;        /** position array */
127	>	vector<Vector3d> velocity;        /** velocity array */
128	>	vector<Vector3d> force;           /** force array */
129	>	vector<RotMat3x3d> aMat;          /** rotation matrix array */
130	>	vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
131	>	vector<Vector3d> torque;          /** torque array */
132	>	vector<RealType> particlePot;     /** particle potential arrray */
133	>	vector<RealType> density;         /** electron density */
134	>	vector<RealType> functional;      /** density functional */
135	>	vector<RealType> functionalDerivative; /** derivative of functional */
136	>	vector<Vector3d> dipole;          /** space-frame dipole vector */
137	>	vector<Mat3x3d>  quadrupole;      /** space-frame quadrupole tensor */
138	>	vector<Vector3d> electricField;   /** local electric field */
139	>	vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
140	>	vector<RealType> flucQPos;        /** fluctuating charges */
141	>	vector<RealType> flucQVel;        /** fluctuating charge velocities */
142	>	vector<RealType> flucQFrc;        /** fluctuating charge forces */
143
144	+	static int getBytesPerStuntDouble(int layout);
145
146	<	DataStorage();
80	<	DataStorage(int size, int storageLayout = 255);
81	<	/** return the size of this DataStorage. */
82	<	int getSize();
83	<	/**
84	<	* Changes the size of this DataStorage.
85	<	* @param size new size of this DataStorage
86	<	*/
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	<	double *getArrayPointer(int whichArray);
146	>	private:
147
148	<	std::vector<Vector3d> position;               /** position array */
149	<	std::vector<Vector3d> velocity;               /** velocity array */
150	<	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<double> 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	<	private:
122	<
123	<	double* internalGetArrayPointer(std::vector<Vector3d>& v);
148	>	RealType* internalGetArrayPointer(vector<Vector3d>& v);
149	>	RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
150	>	RealType* internalGetArrayPointer(vector<RealType>& v);
151
152	<	double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
153	<	double* internalGetArrayPointer(std::vector<double>& v);
127	<
128	<	template<typename T>
129	<	void internalResize(std::vector<T>& v, int newSize);
152	>	template<typename T>
153	>	void internalResize(std::vector<T>& v, int newSize);
154
155	<	template<typename T>
156	<	void internalCopy(std::vector<T>& v, int source,  int num, int target);
155	>	template<typename T>
156	>	void internalCopy(std::vector<T>& v, int source,  int num, int target);
157
158	<	int size_;
159	<	int storageLayout_;
158	>	int size_;
159	>	int storageLayout_;
160
161	<	};
161	>	};
162
163		}
164		#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.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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