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

Comparing trunk/src/integrators/Integrator.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	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
46	–	* @time 13:25am
47		* @version 1.0
48		*/
49
#	Line 52 | Line 52
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		/**
#	Line 75 | Line 79 | namespace oopse {
79		doIntegrate();
80		}
81
82	<	void update() {
83	<	doUpdate();
82	>	void updateSizes() {
83	>	doUpdateSizes();
84	>	flucQ_->updateSizes();
85		}
86
87		void setForceManager(ForceManager* forceMan) {
88	+
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		void setVelocitizer(Velocitizer* velocitizer) {
100	<	if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
100	>	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
101		delete velocitizer_;
102		}
103	<	velocitizer_  = velocitizer;
103	>	velocitizer_ = velocitizer;
104		}
105	<
105	>
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	>	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 doUpdate() {}
137	>	virtual void doUpdateSizes() {}
138
139		void saveConservedQuantity() {
140	<	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
140	>	snap->setConservedQuantity( calcConservedQuantity() );
141		}
142
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;
114	–	Velocitizer* velocitizer_;
155		bool needVelocityScaling;
156		RealType targetScalingTemp;
157	+
158	+	bool useRNEMD;
159
160	+	Stats* stats;
161		DumpWriter* dumpWriter;
162		StatWriter* statWriter;
120	–	RestWriter* restWriter;
163		Thermo thermo;
164
165		RealType runTime;
#	Line 125 | Line 167 | namespace oopse {
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:

Comparing trunk/src/integrators/Integrator.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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