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

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 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		/**
#	Line 50 | Line 51
51		#include "integrators/VelocityVerletIntegrator.hpp"
52		#include "integrators/DLM.hpp"
53		#include "utils/StringUtils.hpp"
54	+	#include "utils/ProgressBar.hpp"
55
56	<	namespace oopse {
57	<	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56	>	namespace OpenMD {
57	>	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
58		dt2 = 0.5 * dt;
59	<	rotAlgo = new DLM();
60	<	rattle = new Rattle(info);
61	<	}
62	<
63	<	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
64	<	delete rotAlgo;
65	<	delete rattle;
66	<	}
67	<
68	<	void VelocityVerletIntegrator::initialize(){
69	<
68	<	forceMan_->init();
69	<
70	<	// remove center of mass drift velocity (in case we passed in a configuration
71	<	// that was drifting
59	>	}
60	>
61	>	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	>	}
63	>
64	>	void VelocityVerletIntegrator::initialize(){
65	>
66	>	forceMan_->initialize();
67	>
68	>	// remove center of mass drift velocity (in case we passed in a
69	>	// configuration that was drifting)
70		velocitizer_->removeComDrift();
71
72	+	// find the initial fluctuating charges.
73	+	flucQ_->initialize();
74	+
75		// initialize the forces before the first step
76	<	calcForce(true, true);
77	<
78	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
76	>	calcForce();
77	>
78	>	// execute the constraint algorithm to make sure that the system is
79	>	// constrained at the very beginning
80		if (info_->getNGlobalConstraints() > 0) {
81	<	rattle->constraintA();
82	<	calcForce(true, true);
83	<	rattle->constraintB();
84	<	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
81	>	rattle_->constraintA();
82	>	calcForce();
83	>	rattle_->constraintB();
84	>	//copy the current snapshot to previous snapshot
85	>	info_->getSnapshotManager()->advance();
86		}
87	<
87	>
88		if (needVelocityScaling) {
89	<	velocitizer_->velocitize(targetScalingTemp);
89	>	velocitizer_->velocitize(targetScalingTemp);
90		}
91
92		dumpWriter = createDumpWriter();
93	<	eorWriter = createEorWriter();
93	>
94		statWriter = createStatWriter();
95	+
96	+	dumpWriter->writeDumpAndEor();
97
98	<	dumpWriter->writeDump();
99	<	eorWriter->writeDump();
95	<
98	>	progressBar = new ProgressBar();
99	>
100		//save statistics, before writeStat,  we must save statistics
97	–	thermo.saveStat();
101		saveConservedQuantity();
102	<	statWriter->writeStat(currentSnapshot_->statData);
102	>	stats->collectStats();
103
104	<	currSample = sampleTime + currentSnapshot_->getTime();
105	<	currStatus =  statusTime + currentSnapshot_->getTime();;
106	<	currThermal = thermalTime +  + currentSnapshot_->getTime();
104	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
105	>	rnemd_->getStarted();
106	>
107	>	statWriter->writeStat();
108	>
109	>	currSample = sampleTime + snap->getTime();
110	>	currStatus =  statusTime + snap->getTime();
111	>	currThermal = thermalTime + snap->getTime();
112	>	if (needReset) {
113	>	currReset = resetTime + snap->getTime();
114	>	}
115	>	if (simParams->getRNEMDParameters()->getUseRNEMD()){
116	>	currRNEMD = RNEMD_exchangeTime + snap->getTime();
117	>	}
118		needPotential = false;
119		needStress = false;
120	<
121	<	}
122	<
123	<	void VelocityVerletIntegrator::doIntegrate() {
124	<
111	<
120	>
121	>	}
122	>
123	>	void VelocityVerletIntegrator::doIntegrate() {
124	>
125		initialize();
126	+
127	+	while (snap->getTime() < runTime) {
128	+	preStep();
129	+	integrateStep();
130	+	postStep();
131	+	}
132	+	finalize();
133	+	}
134
114	–	while (currentSnapshot_->getTime() < runTime) {
115	–
116	–	preStep();
135
136	<	integrateStep();
137	<
138	<	postStep();
139	<
136	>	void VelocityVerletIntegrator::preStep() {
137	>	RealType difference = snap->getTime() + dt - currStatus;
138	>
139	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
140	>	needPotential = true;
141	>	needStress = true;
142		}
143	+	}
144
145	<	finalize();
145	>	void VelocityVerletIntegrator::postStep() {
146	>
147	>	//save snapshot
148	>	info_->getSnapshotManager()->advance();
149	>
150	>	//increase time
151	>	snap->increaseTime(dt);
152	>
153	>	if (needVelocityScaling) {
154	>	if (snap->getTime() >= currThermal) {
155	>	velocitizer_->velocitize(targetScalingTemp);
156	>	currThermal += thermalTime;
157	>	}
158	>	}
159	>	if (useRNEMD) {
160	>	if (snap->getTime() >= currRNEMD) {
161	>	rnemd_->doRNEMD();
162	>	currRNEMD += RNEMD_exchangeTime;
163	>	}
164	>	rnemd_->collectData();
165	>	}
166
167	<	}
167	>	if (snap->getTime() >= currSample) {
168	>	dumpWriter->writeDumpAndEor();
169	>
170	>	currSample += sampleTime;
171	>	}
172	>
173	>	if (snap->getTime() >= currStatus) {
174	>	//save statistics, before writeStat,  we must save statistics
175	>	stats->collectStats();
176	>	saveConservedQuantity();
177
178	+	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
179	+	rnemd_->writeOutputFile();
180	+	}
181
182	<	void VelocityVerletIntegrator::preStep() {
130	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
182	>	statWriter->writeStat();
183
184	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
185	<	needPotential = true;
134	<	needStress = true;
135	<	}
184	>	progressBar->setStatus(snap->getTime(), runTime);
185	>	progressBar->update();
186
187	<	}
187	>	needPotential = false;
188	>	needStress = false;
189	>	currStatus += statusTime;
190	>	}
191	>
192	>	if (needReset && snap->getTime() >= currReset) {
193	>	resetIntegrator();
194	>	currReset += resetTime;
195	>	}
196	>	}
197
139	–	void VelocityVerletIntegrator::postStep() {
198
199	<	//save snapshot
200	<	info_->getSnapshotManager()->advance();
201	<
202	<	//increase time
145	<	currentSnapshot_->increaseTime(dt);
146	<
147	<	if (needVelocityScaling) {
148	<	if (currentSnapshot_->getTime() >= currThermal) {
149	<	velocitizer_->velocitize(targetScalingTemp);
150	<	currThermal += thermalTime;
151	<	}
152	<	}
153	<
154	<	if (currentSnapshot_->getTime() >= currSample) {
155	<	dumpWriter->writeDump();
156	<	eorWriter->writeDump();
157	<	currSample += sampleTime;
158	<	}
159	<
160	<	if (currentSnapshot_->getTime() >= currStatus) {
161	<	//save statistics, before writeStat,  we must save statistics
162	<	thermo.saveStat();
163	<	saveConservedQuantity();
164	<	statWriter->writeStat(currentSnapshot_->statData);
165	<
166	<	needPotential = false;
167	<	needStress = false;
168	<	currStatus += statusTime;
169	<	}
170	<
171	<
172	<	}
173	<
174	<
175	<	void VelocityVerletIntegrator::finalize() {
176	<
177	<	dumpWriter->writeDump();
178	<	eorWriter->writeDump();
179	<
199	>	void VelocityVerletIntegrator::finalize() {
200	>	dumpWriter->writeEor();
201	>	rnemd_->writeOutputFile();
202	>
203		delete dumpWriter;
181	–	delete eorWriter;
204		delete statWriter;
205	<
205	>
206		dumpWriter = NULL;
185	–	eorWriter = NULL;
207		statWriter = NULL;
208	<
188	<	}
208	>	}
209
210	<	void VelocityVerletIntegrator::integrateStep() {
211	<
210	>	void VelocityVerletIntegrator::integrateStep() {
211	>
212		moveA();
213	<	calcForce(needPotential, needStress);
213	>	calcForce();
214		moveB();
215	<	}
215	>	}
216
217
218	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
219	<	bool needStress) {
220	<	forceMan_->calcForces(needPotential, needStress);
221	<	}
218	>	void VelocityVerletIntegrator::calcForce() {
219	>	forceMan_->calcForces();
220	>	flucQ_->applyConstraints();
221	>	}
222
223	<	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224	<	return new DumpWriter(info_, info_->getDumpFileName());
225	<	}
223	>	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224	>	return new DumpWriter(info_);
225	>	}
226
227	<	DumpWriter* VelocityVerletIntegrator::createEorWriter() {
228	<	return new DumpWriter(info_, getPrefix(info_->getDumpFileName()) + ".eor");
229	<	}
227	>	StatWriter* VelocityVerletIntegrator::createStatWriter() {
228	>
229	>	stats = new Stats(info_);
230	>	statWriter = new StatWriter(info_->getStatFileName(), stats);
231	>
232	>	return statWriter;
233	>	}
234
235	<	StatWriter* VelocityVerletIntegrator::createStatWriter() {
212	<	return new StatWriter(info_->getStatFileName());
213	<	}
214	<
215	<
216	<	} //end namespace oopse
235	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

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