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root/OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.hpp

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.hpp (file contents), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.hpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file VelocityVerletIntegrator.hpp
45	<	* @author tlin
46	<	* @date 11/08/2004
47	<	* @time 13:25am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file VelocityVerletIntegrator.hpp
45	>	* @author tlin
46	>	* @date 11/08/2004
47	>	* @time 13:25am
48	>	* @version 1.0
49	>	*/
50
51		#ifndef INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
52		#define INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP
#	Line 53 | Line 54
54		#include "integrators/Integrator.hpp"
55		#include "integrators/RotationAlgorithm.hpp"
56		#include "constraints/Rattle.hpp"
57	<	namespace oopse {
57	>	#include "utils/ProgressBar.hpp"
58	>	namespace OpenMD {
59
60	<	/**
61	<	* @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
62	<	* @brief  Velocity-Verlet Family Integrator
63	<	* Template pattern is used in VelocityVerletIntegrator class.
64	<	*/
65	<	class VelocityVerletIntegrator : public Integrator {
66	<	public:
67	<	virtual ~VelocityVerletIntegrator();
60	>	/**
61	>	* @class VelocityVerletIntegrator VelocityVerletIntegrator.hpp "integrators/VelocityVerletIntegrator.hpp"
62	>	* @brief  Velocity-Verlet Family Integrator
63	>	* Template pattern is used in VelocityVerletIntegrator class.
64	>	*/
65	>	class VelocityVerletIntegrator : public Integrator {
66	>	public:
67	>	virtual ~VelocityVerletIntegrator();
68
69	<	void setRotationAlgorithm(RotationAlgorithm* algo) {
70	<	if (algo != rotAlgo && rotAlgo != NULL){
71	<	delete rotAlgo;
72	<	}
69	>	void setRotationAlgorithm(RotationAlgorithm* algo) {
70	>	if (algo != rotAlgo && rotAlgo != NULL){
71	>	delete rotAlgo;
72	>	}
73
74	<	rotAlgo = algo;
75	<	}
74	>	rotAlgo = algo;
75	>	}
76
77	<	protected:
77	>	protected:
78
79	<	VelocityVerletIntegrator(SimInfo* info);
79	>	VelocityVerletIntegrator(SimInfo* info);
80
81	<	virtual void doIntegrate();
81	>	virtual void doIntegrate();
82
83	<	virtual void initialize();
83	>	virtual void initialize();
84
85	<	virtual void preStep();
85	>	virtual void preStep();
86
87	<	virtual void integrateStep();
87	>	virtual void integrateStep();
88
89	<	virtual void postStep();
89	>	virtual void postStep();
90
91	<	virtual void finalize();
91	>	virtual void finalize();
92
93	<	RotationAlgorithm* rotAlgo;
94	<	Rattle* rattle;
95	<	double dt2;
93	>	virtual void resetIntegrator() {}
94	>
95	>	RotationAlgorithm* rotAlgo;
96	>	Rattle* rattle;
97	>	RealType dt2;
98
99	<	double currSample;
100	<	double currStatus;
101	<	double currThermal;
99	>	RealType currSample;
100	>	RealType currStatus;
101	>	RealType currThermal;
102	>	RealType currReset;
103	>	RealType currRNEMD;
104
105	<	private:
105	>	private:
106
107	<	virtual void calcForce(bool needPotential, bool needStress);
107	>	virtual void calcForce();
108
109	<	virtual void moveA() = 0;
109	>	virtual void moveA() = 0;
110
111	<	virtual void moveB() = 0;
111	>	virtual void moveB() = 0;
112
113	<	virtual double calcConservedQuantity() = 0;
113	>	virtual RealType calcConservedQuantity() = 0;
114
115	<	virtual DumpWriter* createDumpWriter();
115	>	virtual DumpWriter* createDumpWriter();
116
117	<	virtual StatWriter* createStatWriter();
112	<
113	<	virtual RestWriter* createRestWriter();
117	>	virtual StatWriter* createStatWriter();
118
119	<	};
119	>	ProgressBar* progressBar;
120
121	<	} //end namespace oopse
121	>	};
122	>
123	>	} //end namespace OpenMD
124		#endif //INTEGRATORS_VELOCITYVERLETINTEGRATOR_HPP

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.hpp (property svn:keywords), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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