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Comparing trunk/src/brains/DataStorage.hpp (file contents):
Revision 155 by tim, Tue Oct 26 22:19:22 2004 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 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, 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	<
42	>
43		/**
44		* @file Vector.hpp
45		* @author Teng Lin
#	Line 37 | Line 54
54		#include <math/Vector3.hpp>
55		#include <math/SquareMatrix3.hpp>
56
57	<	using 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	+	dslSitePotential = 131072
88	+	};
89
90	<
91	<	//forward declaration
92	<	class Snapshot;
93	<	class StuntDouble;
47	<	class DataStorageTestCase;
90	>	DataStorage();
91	>	DataStorage(int size, int storageLayout = 0);
92	>	/** return the size of this DataStorage. */
93	>	int getSize();
94		/**
95	<	* @class DataStorage
96	<	* @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
95	>	* Changes the size of this DataStorage.
96	>	* @param newSize new size of this DataStorage
97		*/
98	<	class DataStorage {
99	<	public:
98	>	void resize(int newSize);
99	>	/**
100	>	* Reallocates memory manually.
101	>	*
102	>	* The main reason for using reserve() is efficiency if you know
103	>	* the capacity to which your vector must eventually grow,
104	>	* then it is usually more efficient to allocate that memory all
105	>	* at once.
106	>	*/
107	>	void reserve(int size);
108	>	/**
109	>	* Copies data inside DataStorage class.
110	>	*
111	>	* Copy function actually calls copy for every vector in
112	>	* DataStorage class.  One Precondition of copy is that
113	>	* target is not within the range [source, soruce + num]
114	>	*
115	>	* @param source
116	>	* @param num number of element to be moved
117	>	* @param target
118	>	*/
119	>	void copy(int source, int num, int target);
120	>	/** Returns the storage layout  */
121	>	int getStorageLayout();
122	>	/** Sets the storage layout  */
123	>	void setStorageLayout(int layout);
124	>	/** Returns the pointer of internal array */
125	>	RealType *getArrayPointer(int whichArray);
126
127	<	enum{
128	<	dslPosition = 1,
129	<	dslVelocity = 2,
130	<	dslAmat = 4,
131	<	dslAngularMomentum = 8,
132	<	dslUnitVector = 16,
133	<	dslZAngle = 32,
134	<	dslForce = 64,
135	<	dslTorque = 128
136	<	};
127	>	vector<Vector3d> position;        /** position array */
128	>	vector<Vector3d> velocity;        /** velocity array */
129	>	vector<Vector3d> force;           /** force array */
130	>	vector<RotMat3x3d> aMat;          /** rotation matrix array */
131	>	vector<Vector3d> angularMomentum; /** angular momentum array (body-fixed) */
132	>	vector<Vector3d> torque;          /** torque array */
133	>	vector<RealType> particlePot;     /** particle potential arrray */
134	>	vector<RealType> density;         /** electron density */
135	>	vector<RealType> functional;      /** density functional */
136	>	vector<RealType> functionalDerivative; /** derivative of functional */
137	>	vector<Vector3d> dipole;          /** space-frame dipole vector */
138	>	vector<Mat3x3d>  quadrupole;      /** space-frame quadrupole tensor */
139	>	vector<Vector3d> electricField;   /** local electric field */
140	>	vector<RealType> skippedCharge;   /** charge skipped during normal pairwise calculation */
141	>	vector<RealType> flucQPos;        /** fluctuating charges */
142	>	vector<RealType> flucQVel;        /** fluctuating charge velocities */
143	>	vector<RealType> flucQFrc;        /** fluctuating charge forces */
144	>	vector<RealType> sitePotential;   /** electrostatic site potentials */
145
146	+	static int getBytesPerStuntDouble(int layout);
147
148	<	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:
148	>	private:
149
150	<
151	<	double* internalGetArrayPointer(std::vector<Vector3d>& v);
150	>	RealType* internalGetArrayPointer(vector<Vector3d>& v);
151	>	RealType* internalGetArrayPointer(vector<Mat3x3d>& v);
152	>	RealType* internalGetArrayPointer(vector<RealType>& v);
153
154	<	double* internalGetArrayPointer(std::vector<RotMat3x3d>& v);
155	<	double* internalGetArrayPointer(std::vector<double>& v);
109	<
110	<	template<typename T>
111	<	void internalResize(std::vector<T>& v, int newSize);
154	>	template<typename T>
155	>	void internalResize(std::vector<T>& v, int newSize);
156
157	<	template<typename T>
158	<	void interalCopy(std::vector<T>& v, int source,  int num, int target);
157	>	template<typename T>
158	>	void internalCopy(std::vector<T>& v, int source,  int num, int target);
159
160	<	int size_;
161	<	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;/** velocity array */
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	<	};
160	>	int size_;
161	>	int storageLayout_;
162
163	+	};
164
165	+	}
166		#endif //BRAINS_DATASTORAGE_HPP

Comparing trunk/src/brains/DataStorage.hpp (property svn:keywords):
Revision 155 by tim, Tue Oct 26 22:19:22 2004 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

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

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