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root/OpenMD/trunk/src/integrators/VelocityVerletIntegrator.cpp

Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 2074 by gezelter, Sun Mar 8 00:02:29 2015 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;
57	–	rotAlgo = new DLM();
58	–	rattle = new Rattle(info);
58		}
59
60		VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	–	delete rotAlgo;
63	–	delete rattle;
61		}
62
63		void VelocityVerletIntegrator::initialize(){
64
65	<	forceMan_->init();
65	>	forceMan_->initialize();
66
67	<	// remove center of mass drift velocity (in case we passed in a configuration
68	<	// that was drifting
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);
75	>	calcForce();
76
77	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
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
87		if (needVelocityScaling) {
88		velocitizer_->velocitize(targetScalingTemp);
89		}
90
91	<	dumpWriter = createDumpWriter();
92	<
91	<	statWriter = createStatWriter();
92	<
93	<	if (simParams->getUseSolidThermInt()) {
94	<	restWriter = createRestWriter();
95	<	restWriter->writeZangle();
96	<	}
97	<
91	>	dumpWriter = createDumpWriter();
92	>	statWriter = createStatWriter();
93		dumpWriter->writeDumpAndEor();
94	<
95	<
94	>
95	>	progressBar = new ProgressBar();
96	>
97		//save statistics, before writeStat,  we must save statistics
102	–	thermo.saveStat();
98		saveConservedQuantity();
99	<	statWriter->writeStat(currentSnapshot_->statData);
99	>	stats->collectStats();
100	>
101	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
102	>	rnemd_->getStarted();
103	>
104	>	statWriter->writeStat();
105
106	<	currSample = sampleTime + currentSnapshot_->getTime();
107	<	currStatus =  statusTime + currentSnapshot_->getTime();;
108	<	currThermal = thermalTime +  + currentSnapshot_->getTime();
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
112	–	}
113	–
114	–	void VelocityVerletIntegrator::doIntegrate() {
115	–
116	–
117	–	initialize();
118	–
119	–	while (currentSnapshot_->getTime() < runTime) {
120	–
121	–	preStep();
122	–
123	–	integrateStep();
124	–
125	–	postStep();
126	–
118		}
119	+
120	+	void VelocityVerletIntegrator::doIntegrate() {
121
122	<	finalize();
122	>	initialize();
123
124	<	}
124	>	while (snap->getTime() < runTime) {
125	>	preStep();
126	>	integrateStep();
127	>	postStep();
128	>	}
129	>	finalize();
130	>	}
131
132
133	<	void VelocityVerletIntegrator::preStep() {
134	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
133	>	void VelocityVerletIntegrator::preStep() {
134	>	RealType difference = snap->getTime() + dt - currStatus;
135
136	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
137	<	needPotential = true;
138	<	needStress = true;
136	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
137	>	needPotential = true;
138	>	needStress = true;
139	>	}
140		}
141	–
142	–	}
141
142	<	void VelocityVerletIntegrator::postStep() {
143	<
144	<	//save snapshot
145	<	info_->getSnapshotManager()->advance();
146	<
147	<	//increase time
148	<	currentSnapshot_->increaseTime(dt);
149	<
152	<	if (needVelocityScaling) {
153	<	if (currentSnapshot_->getTime() >= currThermal) {
154	<	velocitizer_->velocitize(targetScalingTemp);
155	<	currThermal += thermalTime;
142	>	void VelocityVerletIntegrator::postStep() {
143	>
144	>
145	>	if (needVelocityScaling) {
146	>	if (snap->getTime() >= currThermal) {
147	>	velocitizer_->velocitize(targetScalingTemp);
148	>	currThermal += thermalTime;
149	>	}
150		}
151	<	}
152	<
153	<	if (currentSnapshot_->getTime() >= currSample) {
154	<	dumpWriter->writeDumpAndEor();
151	>	if (useRNEMD) {
152	>	if (snap->getTime() >= currRNEMD) {
153	>	rnemd_->doRNEMD();
154	>	currRNEMD += RNEMD_exchangeTime;
155	>	}
156	>	rnemd_->collectData();
157	>	}
158
159	<	if (simParams->getUseSolidThermInt())
160	<	restWriter->writeZangle();
159	>	if (snap->getTime() >= currSample) {
160	>	dumpWriter->writeDumpAndEor();
161	>
162	>	currSample += sampleTime;
163	>	}
164
165	<	currSample += sampleTime;
166	<	}
167	<
168	<	if (currentSnapshot_->getTime() >= currStatus) {
169	<	//save statistics, before writeStat,  we must save statistics
170	<	thermo.saveStat();
171	<	saveConservedQuantity();
172	<	statWriter->writeStat(currentSnapshot_->statData);
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	>	statWriter->writeStat();
175	>
176	>	progressBar->setStatus(snap->getTime(), runTime);
177	>	progressBar->update();
178	>
179	>	needPotential = false;
180	>	needStress = false;
181	>	currStatus += statusTime;
182	>	}
183
184	<	needPotential = false;
185	<	needStress = false;
186	<	currStatus += statusTime;
187	<	}
184	>	if (needReset && snap->getTime() >= currReset) {
185	>	resetIntegrator();
186	>	currReset += resetTime;
187	>	}
188	>	//save snapshot
189	>	info_->getSnapshotManager()->advance();
190
191	<
192	<	}
191	>	//increase time
192	>	snap->increaseTime(dt);
193
194	+	}
195
196	<	void VelocityVerletIntegrator::finalize() {
197	<	dumpWriter->writeEor();
196	>
197	>	void VelocityVerletIntegrator::finalize() {
198	>	dumpWriter->writeEor();
199	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
200	>	rnemd_->writeOutputFile();
201	>	}
202	>	progressBar->setStatus(runTime, runTime);
203	>	progressBar->update();
204	>
205	>	delete dumpWriter;
206	>	delete statWriter;
207
208	<	if (simParams->getUseSolidThermInt()) {
209	<	restWriter->writeZangle();
188	<	delete restWriter;
189	<	restWriter = NULL;
208	>	dumpWriter = NULL;
209	>	statWriter = NULL;
210		}
191	–
192	–	delete dumpWriter;
193	–	delete statWriter;
194	–
195	–	dumpWriter = NULL;
196	–	statWriter = NULL;
197	–
198	–	}
211
212	<	void VelocityVerletIntegrator::integrateStep() {
212	>	void VelocityVerletIntegrator::integrateStep() {
213
214	<	moveA();
215	<	calcForce(needPotential, needStress);
216	<	moveB();
217	<	}
214	>	moveA();
215	>	calcForce();
216	>	moveB();
217	>	}
218
219
220	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
221	<	bool needStress) {
222	<	forceMan_->calcForces(needPotential, needStress);
223	<	}
220	>	void VelocityVerletIntegrator::calcForce() {
221	>	forceMan_->calcForces();
222	>	flucQ_->applyConstraints();
223	>	}
224
225	<	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
226	<	return new DumpWriter(info_);
227	<	}
225	>	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
226	>	return new DumpWriter(info_);
227	>	}
228
229	<	StatWriter* VelocityVerletIntegrator::createStatWriter() {
230	<	// if solidThermInt is true, add extra information to the statfile
231	<	if (simParams->getUseSolidThermInt()){
232	<	StatsBitSet mask;
233	<	mask.set(Stats::TIME);
234	<	mask.set(Stats::TOTAL_ENERGY);
223	<	mask.set(Stats::POTENTIAL_ENERGY);
224	<	mask.set(Stats::KINETIC_ENERGY);
225	<	mask.set(Stats::TEMPERATURE);
226	<	mask.set(Stats::PRESSURE);
227	<	mask.set(Stats::CONSERVED_QUANTITY);
228	<	mask.set(Stats::VRAW);
229	<	mask.set(Stats::VHARM);
230	<	return new StatWriter(info_->getStatFileName(), mask);
229	>	StatWriter* VelocityVerletIntegrator::createStatWriter() {
230	>
231	>	stats = new Stats(info_);
232	>	statWriter = new StatWriter(info_->getStatFileName(), stats);
233	>
234	>	return statWriter;
235		}
232	–
233	–	return new StatWriter(info_->getStatFileName());
234	–	}
236
237	<	RestWriter* VelocityVerletIntegrator::createRestWriter(){
237	<	return new RestWriter(info_);
238	<	}
239	<
240	<
241	<	} //end namespace oopse
237	>	} //end namespace OpenMD

Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 2074 by gezelter, Sun Mar 8 00:02:29 2015 UTC

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