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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 1782 by gezelter, Wed Aug 22 02:28:28 2012 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, 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		/**
#	Line 52 | Line 53
53
54		#include "brains/ForceManager.hpp"
55		#include "restraints/ThermoIntegrationForceManager.hpp"
56	+	#include "brains/Stats.hpp"
57		#include "io/DumpWriter.hpp"
58		#include "io/StatWriter.hpp"
59	<	#include "io/RestWriter.hpp"
59	>	#include "integrators/RotationAlgorithm.hpp"
60	>	#include "flucq/FluctuatingChargePropagator.hpp"
61		#include "integrators/Velocitizer.hpp"
62	+	#include "rnemd/RNEMD.hpp"
63	+	#include "constraints/Rattle.hpp"
64
65	<	namespace oopse {
65	>	namespace OpenMD {
66
67
68		/**
#	Line 75 | Line 80 | namespace oopse {
80		doIntegrate();
81		}
82
83	<	void update() {
84	<	doUpdate();
83	>	void updateSizes() {
84	>	doUpdateSizes();
85	>	flucQ_->updateSizes();
86		}
87
88		void setForceManager(ForceManager* forceMan) {
89	+
90		if (forceMan_ != forceMan && forceMan_  != NULL) {
91		delete forceMan_;
92		}
93		forceMan_ = forceMan;
94	+	// forward this on:
95	+	if (flucQ_ != NULL) {
96	+	flucQ_->setForceManager(forceMan_);
97	+	}
98		}
99
100		void setVelocitizer(Velocitizer* velocitizer) {
101	<	if (velocitizer_ != velocitizer && velocitizer_  != NULL) {
101	>	if (velocitizer_ != velocitizer && velocitizer_ != NULL) {
102		delete velocitizer_;
103		}
104	<	velocitizer_  = velocitizer;
104	>	velocitizer_ = velocitizer;
105		}
106	<
106	>
107	>	void setFluctuatingChargePropagator(FluctuatingChargePropagator* prop) {
108	>	if (prop != flucQ_ && flucQ_ != NULL){
109	>	delete flucQ_;
110	>	}
111	>	flucQ_ = prop;
112	>	if (forceMan_ != NULL) {
113	>	flucQ_->setForceManager(forceMan_);
114	>	}
115	>	}
116	>
117	>	void setRotationAlgorithm(RotationAlgorithm* algo) {
118	>	if (algo != rotAlgo_ && rotAlgo_ != NULL){
119	>	delete rotAlgo_;
120	>	}
121	>
122	>	rotAlgo_ = algo;
123	>	}
124	>
125	>	void setRNEMD(RNEMD* rnemd) {
126	>	if (rnemd_ != rnemd && rnemd_  != NULL) {
127	>	delete rnemd_;
128	>	}
129	>	rnemd_ = rnemd;
130	>	}
131	>
132		protected:
133
134		Integrator(SimInfo* info);
135
136		virtual void doIntegrate() = 0;
137
138	<	virtual void doUpdate() {}
138	>	virtual void doUpdateSizes() {}
139
140		void saveConservedQuantity() {
141	<	currentSnapshot_->statData[Stats::CONSERVED_QUANTITY] = calcConservedQuantity();
141	>	snap->setConservedQuantity( calcConservedQuantity() );
142		}
143
144		SimInfo* info_;
145		Globals* simParams;
146		ForceManager* forceMan_;
147	+	RotationAlgorithm* rotAlgo_;
148	+	FluctuatingChargePropagator* flucQ_;
149	+	Rattle* rattle_;
150	+	Velocitizer* velocitizer_;
151	+	RNEMD* rnemd_;
152	+
153		bool needPotential;
154		bool needStress;
155		bool needReset;
114	–	Velocitizer* velocitizer_;
156		bool needVelocityScaling;
157		RealType targetScalingTemp;
158	+
159	+	bool useRNEMD;
160
161	+	Stats* stats;
162		DumpWriter* dumpWriter;
163		StatWriter* statWriter;
120	–	RestWriter* restWriter;
164		Thermo thermo;
165
166		RealType runTime;
#	Line 125 | Line 168 | namespace oopse {
168		RealType statusTime;
169		RealType thermalTime;
170		RealType resetTime;
171	+	RealType RNEMD_exchangeTime;
172		RealType dt;
173
174	<	Snapshot* currentSnapshot_; //During the integration, the address of currentSnapshot Will not change
174	>	Snapshot* snap; // During the integration, the address of snap Will not change
175
176
177		private:

Comparing trunk/src/integrators/Integrator.hpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

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