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

Comparing:
trunk/src/integrators/Integrator.hpp (file contents), Revision 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
branches/development/src/integrators/Integrator.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 Integrator.hpp
45	<	* @author tlin
46	<	* @date 11/08/2004
47	<	* @time 13:25am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file Integrator.hpp
45	>	* @author tlin
46	>	* @date 11/08/2004
47	>	* @time 13:25am
48	>	* @version 1.0
49	>	*/
50
51		#ifndef INTEGRATORS_INTEGRATOR_HPP
52		#define INTEGRATORS_INTEGRATOR_HPP
53
54		#include "brains/ForceManager.hpp"
55	+	#include "restraints/ThermoIntegrationForceManager.hpp"
56		#include "io/DumpWriter.hpp"
57		#include "io/StatWriter.hpp"
58		#include "integrators/Velocitizer.hpp"
59	+	#include "integrators/RNEMD.hpp"
60
61	<	namespace oopse {
61	>	namespace OpenMD {
62
63
64	<	/**
65	<	* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
66	<	* @brief Base class of Integrator
67	<	* @todo document
68	<	*/
69	<	class Integrator {
70	<	public:
64	>	/**
65	>	* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
66	>	* @brief Base class of Integrator
67	>	* @todo document
68	>	*/
69	>	class Integrator {
70	>	public:
71
72	<	virtual ~Integrator();
72	>	virtual ~Integrator();
73
74	<	//avoid public virtual function
75	<	void integrate() {
76	<	doIntegrate();
77	<	}
74	>	//avoid public virtual function
75	>	void integrate() {
76	>	doIntegrate();
77	>	}
78
79	<	void update() {
80	<	doUpdate();
81	<	}
79	>	void update() {
80	>	doUpdate();
81	>	}
82
83	<	void setForceManager(ForceManager* forceMan) {
81	<	if (forceMan_ != forceMan && forceMan_  != NULL) {
82	<	delete forceMan_;
83	<	}
84	<	forceMan_ = forceMan;
85	<	}
83	>	void setForceManager(ForceManager* forceMan) {
84
85	<	void setVelocitizer(Velocitizer* velocitizer) {
86	<	if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
87	<	delete velocitizer_;
88	<	}
89	<	velocitizer_  = velocitizer;
92	<	}
93	<
94	<	protected:
85	>	if (forceMan_ != forceMan && forceMan_  != NULL) {
86	>	delete forceMan_;
87	>	}
88	>	forceMan_ = forceMan;
89	>	}
90
91	<	Integrator(SimInfo* info);
91	>	void setVelocitizer(Velocitizer* velocitizer) {
92	>	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
93	>	delete velocitizer_;
94	>	}
95	>	velocitizer_ = velocitizer;
96	>	}
97
98	<	virtual void doIntegrate() = 0;
98	>	void setRNEMD(RNEMD* rnemd) {
99	>	if (rnemd_ != rnemd && rnemd_  != NULL) {
100	>	delete rnemd_;
101	>	}
102	>	rnemd_ = rnemd;
103	>	}
104	>
105	>	protected:
106
107	<	virtual void doUpdate() {}
107	>	Integrator(SimInfo* info);
108	>
109	>	virtual void doIntegrate() = 0;
110	>
111	>	virtual void doUpdate() {}
112
113	<	void saveConservedQuantity() {
114	<	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
115	<	}
113	>	void saveConservedQuantity() {
114	>	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
115	>	}
116
117	<	SimInfo* info_;
118	<	ForceManager* forceMan_;
119	<	bool needPotential;
120	<	bool needStress;
121	<
122	<	Velocitizer* velocitizer_;
123	<	bool needVelocityScaling;
124	<	double targetScalingTemp;
117	>	SimInfo* info_;
118	>	Globals* simParams;
119	>	ForceManager* forceMan_;
120	>	bool needPotential;
121	>	bool needStress;
122	>	bool needReset;
123	>	Velocitizer* velocitizer_;
124	>	RNEMD* rnemd_;
125	>	bool needVelocityScaling;
126	>	RealType targetScalingTemp;
127	>
128	>	bool useRNEMD;
129
130	<	DumpWriter*dumpWriter;
131	<	DumpWriter* eorWriter;
132	<	StatWriter* statWriter;
118	<	Thermo thermo;
130	>	DumpWriter* dumpWriter;
131	>	StatWriter* statWriter;
132	>	Thermo thermo;
133
134	<	double runTime;
135	<	double sampleTime;
136	<	double statusTime;
137	<	double thermalTime;
138	<	double dt;
134	>	RealType runTime;
135	>	RealType sampleTime;
136	>	RealType statusTime;
137	>	RealType thermalTime;
138	>	RealType resetTime;
139	>	RealType RNEMD_exchangeTime;
140	>	RealType dt;
141
142	<	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
142	>	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
143
144
145	<	private:
145	>	private:
146
147	<	virtual double calcConservedQuantity() = 0;
147	>	virtual RealType calcConservedQuantity() = 0;
148
149	<	virtual DumpWriter* createDumpWriter() = 0;
134	<
135	<	virtual DumpWriter* createEorWriter() = 0;
149	>	virtual DumpWriter* createDumpWriter() = 0;
150
151	<	virtual StatWriter* createStatWriter() = 0;
152	<	};
151	>	virtual StatWriter* createStatWriter() = 0;
152	>	};
153
154
155		}

Comparing:
trunk/src/integrators/Integrator.hpp (property svn:keywords), Revision 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
branches/development/src/integrators/Integrator.hpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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