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root/OpenMD/trunk/src/integrators/Integrator.hpp

Comparing trunk/src/integrators/Integrator.hpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 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	<	/**
44	<	* @file Integrator.hpp
45	<	* @author tlin
46	<	* @date 11/08/2004
47	<	* @time 13:25am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file Integrator.hpp
45	>	* @author tlin
46	>	* @date 11/08/2004
47	>	* @version 1.0
48	>	*/
49
50		#ifndef INTEGRATORS_INTEGRATOR_HPP
51		#define INTEGRATORS_INTEGRATOR_HPP
52
53		#include "brains/ForceManager.hpp"
54		#include "restraints/ThermoIntegrationForceManager.hpp"
55	+	#include "brains/Stats.hpp"
56		#include "io/DumpWriter.hpp"
57		#include "io/StatWriter.hpp"
58	<	#include "io/RestWriter.hpp"
58	>	#include "integrators/RotationAlgorithm.hpp"
59	>	#include "flucq/FluctuatingChargePropagator.hpp"
60		#include "integrators/Velocitizer.hpp"
61	+	#include "rnemd/RNEMD.hpp"
62	+	#include "constraints/Rattle.hpp"
63
64	<	namespace oopse {
64	>	namespace OpenMD {
65
66
67	<	/**
68	<	* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
69	<	* @brief Base class of Integrator
70	<	* @todo document
71	<	*/
72	<	class Integrator {
73	<	public:
67	>	/**
68	>	* @class Integrator Integrator.hpp "integrators/Integrator.hpp"
69	>	* @brief Base class of Integrator
70	>	* @todo document
71	>	*/
72	>	class Integrator {
73	>	public:
74
75	<	virtual ~Integrator();
75	>	virtual ~Integrator();
76
77	<	//avoid public virtual function
78	<	void integrate() {
79	<	doIntegrate();
80	<	}
77	>	//avoid public virtual function
78	>	void integrate() {
79	>	doIntegrate();
80	>	}
81
82	<	void update() {
83	<	doUpdate();
84	<	}
82	>	void updateSizes() {
83	>	doUpdateSizes();
84	>	flucQ_->updateSizes();
85	>	}
86
87	<	void setForceManager(ForceManager* forceMan) {
83	<	if (forceMan_ != forceMan && forceMan_  != NULL) {
84	<	delete forceMan_;
85	<	}
86	<	forceMan_ = forceMan;
87	<	}
87	>	void setForceManager(ForceManager* forceMan) {
88
89	<	void setVelocitizer(Velocitizer* velocitizer) {
90	<	if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
91	<	delete velocitizer_;
92	<	}
93	<	velocitizer_  = velocitizer;
94	<	}
95	<
96	<	protected:
89	>	if (forceMan_ != forceMan && forceMan_  != NULL) {
90	>	delete forceMan_;
91	>	}
92	>	forceMan_ = forceMan;
93	>	// forward this on:
94	>	if (flucQ_ != NULL) {
95	>	flucQ_->setForceManager(forceMan_);
96	>	}
97	>	}
98
99	<	Integrator(SimInfo* info);
99	>	void setVelocitizer(Velocitizer* velocitizer) {
100	>	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
101	>	delete velocitizer_;
102	>	}
103	>	velocitizer_ = velocitizer;
104	>	}
105
106	<	virtual void doIntegrate() = 0;
106	>	void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
107	>	if (prop != flucQ_ && flucQ_ != NULL){
108	>	delete flucQ_;
109	>	}
110	>	flucQ_ = prop;
111	>	if (forceMan_ != NULL) {
112	>	flucQ_->setForceManager(forceMan_);
113	>	}
114	>	}
115
116	<	virtual void doUpdate() {}
116	>	void setRotationAlgorithm(RotationAlgorithm* algo) {
117	>	if (algo != rotAlgo_ && rotAlgo_ != NULL){
118	>	delete rotAlgo_;
119	>	}
120	>
121	>	rotAlgo_ = algo;
122	>	}
123	>
124	>	void setRNEMD(RNEMD* rnemd) {
125	>	if (rnemd_ != rnemd && rnemd_  != NULL) {
126	>	delete rnemd_;
127	>	}
128	>	rnemd_ = rnemd;
129	>	}
130	>
131	>	protected:
132	>
133	>	Integrator(SimInfo* info);
134	>
135	>	virtual void doIntegrate() = 0;
136	>
137	>	virtual void doUpdateSizes() {}
138
139	<	void saveConservedQuantity() {
140	<	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
141	<	}
139	>	void saveConservedQuantity() {
140	>	snap->setConservedQuantity( calcConservedQuantity() );
141	>	}
142
143	<	SimInfo* info_;
144	<	Globals* simParams;
145	<	ForceManager* forceMan_;
146	<	bool needPotential;
147	<	bool needStress;
148	<
149	<	Velocitizer* velocitizer_;
150	<	bool needVelocityScaling;
151	<	double targetScalingTemp;
143	>	SimInfo* info_;
144	>	Globals* simParams;
145	>	ForceManager* forceMan_;
146	>	RotationAlgorithm* rotAlgo_;
147	>	FluctuatingChargePropagator* flucQ_;
148	>	Rattle* rattle_;
149	>	Velocitizer* velocitizer_;
150	>	RNEMD* rnemd_;
151	>
152	>	bool needPotential;
153	>	bool needStress;
154	>	bool needReset;
155	>	bool needVelocityScaling;
156	>	RealType targetScalingTemp;
157	>
158	>	bool useRNEMD;
159
160	<	DumpWriter* dumpWriter;
161	<	StatWriter* statWriter;
162	<	RestWriter* restWriter;
163	<	Thermo thermo;
160	>	Stats* stats;
161	>	DumpWriter* dumpWriter;
162	>	StatWriter* statWriter;
163	>	Thermo thermo;
164
165	<	double runTime;
166	<	double sampleTime;
167	<	double statusTime;
168	<	double thermalTime;
169	<	double dt;
165	>	RealType runTime;
166	>	RealType sampleTime;
167	>	RealType statusTime;
168	>	RealType thermalTime;
169	>	RealType resetTime;
170	>	RealType RNEMD_exchangeTime;
171	>	RealType dt;
172
173	<	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
173	>	Snapshot* snap; // During the integration, the address of snap Will not change
174
175
176	<	private:
176	>	private:
177
178	<	virtual double calcConservedQuantity() = 0;
178	>	virtual RealType calcConservedQuantity() = 0;
179
180	<	virtual DumpWriter* createDumpWriter() = 0;
180	>	virtual DumpWriter* createDumpWriter() = 0;
181
182	<	virtual StatWriter* createStatWriter() = 0;
183	<	};
182	>	virtual StatWriter* createStatWriter() = 0;
183	>	};
184
185
186		}

Comparing trunk/src/integrators/Integrator.hpp (property svn:keywords):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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