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root/OpenMD/trunk/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.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 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 VelocityVerletIntegrator.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 16:16am
47		* @version 1.0
48		*/
49
50		#include "integrators/VelocityVerletIntegrator.hpp"
51		#include "integrators/DLM.hpp"
52		#include "utils/StringUtils.hpp"
53	+	#include "utils/ProgressBar.hpp"
54
55	<	namespace oopse {
56	<	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
55	>	namespace OpenMD {
56	>	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
57		dt2 = 0.5 * dt;
58	<	rotAlgo = new DLM();
59	<	rattle = new Rattle(info);
60	<	}
61	<
62	<	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
63	<	delete rotAlgo;
64	<	delete rattle;
65	<	}
66	<
67	<	void VelocityVerletIntegrator::initialize(){
68	<
68	<	forceMan_->init();
69	<
70	<	// remove center of mass drift velocity (in case we passed in a configuration
71	<	// that was drifting
58	>	}
59	>
60	>	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61	>	}
62	>
63	>	void VelocityVerletIntegrator::initialize(){
64	>
65	>	forceMan_->initialize();
66	>
67	>	// remove center of mass drift velocity (in case we passed in a
68	>	// configuration that was drifting)
69		velocitizer_->removeComDrift();
70
71	+	// find the initial fluctuating charges.
72	+	flucQ_->initialize();
73	+
74		// initialize the forces before the first step
75	<	calcForce(true, true);
76	<
77	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
75	>	calcForce();
76	>
77	>	// execute the constraint algorithm to make sure that the system is
78	>	// constrained at the very beginning
79		if (info_->getNGlobalConstraints() > 0) {
80	<	rattle->constraintA();
81	<	calcForce(true, true);
82	<	rattle->constraintB();
83	<	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
80	>	rattle_->constraintA();
81	>	calcForce();
82	>	rattle_->constraintB();
83	>	//copy the current snapshot to previous snapshot
84	>	info_->getSnapshotManager()->advance();
85		}
86	<
86	>
87		if (needVelocityScaling) {
88	<	velocitizer_->velocitize(targetScalingTemp);
88	>	velocitizer_->velocitize(targetScalingTemp);
89		}
90
91	<	dumpWriter = createDumpWriter();
92	<	eorWriter = createEorWriter();
93	<	statWriter = createStatWriter();
91	>	dumpWriter = createDumpWriter();
92	>	statWriter = createStatWriter();
93	>	dumpWriter->writeDumpAndEor();
94
95	<	dumpWriter->writeDump();
96	<	eorWriter->writeDump();
95	<
95	>	progressBar = new ProgressBar();
96	>
97		//save statistics, before writeStat,  we must save statistics
97	–	thermo.saveStat();
98		saveConservedQuantity();
99	<	statWriter->writeStat(currentSnapshot_->statData);
99	>	stats->collectStats();
100
101	<	currSample = sampleTime + currentSnapshot_->getTime();
102	<	currStatus =  statusTime + currentSnapshot_->getTime();;
103	<	currThermal = thermalTime +  + currentSnapshot_->getTime();
101	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
102	>	rnemd_->getStarted();
103	>
104	>	statWriter->writeStat();
105	>
106	>	currSample = sampleTime + snap->getTime();
107	>	currStatus =  statusTime + snap->getTime();
108	>	currThermal = thermalTime + snap->getTime();
109	>	if (needReset) {
110	>	currReset = resetTime + snap->getTime();
111	>	}
112	>	if (simParams->getRNEMDParameters()->getUseRNEMD()){
113	>	currRNEMD = RNEMD_exchangeTime + snap->getTime();
114	>	}
115		needPotential = false;
116		needStress = false;
117	<
118	<	}
119	<
120	<	void VelocityVerletIntegrator::doIntegrate() {
121	<
111	<
117	>
118	>	}
119	>
120	>	void VelocityVerletIntegrator::doIntegrate() {
121	>
122		initialize();
123	+
124	+	while (snap->getTime() < runTime) {
125	+	preStep();
126	+	integrateStep();
127	+	postStep();
128	+	}
129	+	finalize();
130	+	}
131
114	–	while (currentSnapshot_->getTime() < runTime) {
115	–
116	–	preStep();
132
133	<	integrateStep();
134	<
135	<	postStep();
136	<
133	>	void VelocityVerletIntegrator::preStep() {
134	>	RealType difference = snap->getTime() + dt - currStatus;
135	>
136	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
137	>	needPotential = true;
138	>	needStress = true;
139		}
140	+	}
141
142	<	finalize();
142	>	void VelocityVerletIntegrator::postStep() {
143	>
144	>
145	>	if (needVelocityScaling) {
146	>	if (snap->getTime() >= currThermal) {
147	>	velocitizer_->velocitize(targetScalingTemp);
148	>	currThermal += thermalTime;
149	>	}
150	>	}
151	>	if (useRNEMD) {
152	>	if (snap->getTime() >= currRNEMD) {
153	>	rnemd_->doRNEMD();
154	>	currRNEMD += RNEMD_exchangeTime;
155	>	}
156	>	rnemd_->collectData();
157	>	}
158
159	<	}
159	>	if (snap->getTime() >= currSample) {
160	>	dumpWriter->writeDumpAndEor();
161	>
162	>	currSample += sampleTime;
163	>	}
164	>
165	>	if (snap->getTime() >= currStatus) {
166	>	//save statistics, before writeStat,  we must save statistics
167	>	saveConservedQuantity();
168	>	stats->collectStats();
169
170	+	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
171	+	rnemd_->writeOutputFile();
172	+	}
173
174	<	void VelocityVerletIntegrator::preStep() {
130	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
174	>	statWriter->writeStat();
175
176	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
177	<	needPotential = true;
134	<	needStress = true;
135	<	}
176	>	progressBar->setStatus(snap->getTime(), runTime);
177	>	progressBar->update();
178
179	<	}
179	>	needPotential = false;
180	>	needStress = false;
181	>	currStatus += statusTime;
182	>	}
183	>
184	>	if (needReset && snap->getTime() >= currReset) {
185	>	resetIntegrator();
186	>	currReset += resetTime;
187	>	}
188	>	//save snapshot
189	>	info_->getSnapshotManager()->advance();
190	>
191	>	//increase time
192	>	snap->increaseTime(dt);
193
194	<	void VelocityVerletIntegrator::postStep() {
194	>	}
195
141	–	//save snapshot
142	–	info_->getSnapshotManager()->advance();
196
197	<	//increase time
198	<	currentSnapshot_->increaseTime(dt);
199	<
200	<	if (needVelocityScaling) {
201	<	if (currentSnapshot_->getTime() >= currThermal) {
202	<	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	<
197	>	void VelocityVerletIntegrator::finalize() {
198	>	dumpWriter->writeEor();
199	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
200	>	rnemd_->writeOutputFile();
201	>	}
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.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 2013 UTC

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