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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 1718 by gezelter, Thu May 24 01:29:59 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
101		thermo.saveStat();
102		saveConservedQuantity();
103	<	statWriter->writeStat(currentSnapshot_->statData);
103	>	if (simParams->getUseRNEMD())
104	>	rnemd_->getStarted();
105
106	+	statWriter->writeStat(currentSnapshot_->statData);
107	+
108		currSample = sampleTime + currentSnapshot_->getTime();
109	<	currStatus =  statusTime + currentSnapshot_->getTime();;
110	<	currThermal = thermalTime +  + currentSnapshot_->getTime();
109	>	currStatus =  statusTime + currentSnapshot_->getTime();
110	>	currThermal = thermalTime + currentSnapshot_->getTime();
111	>	if (needReset) {
112	>	currReset = resetTime + currentSnapshot_->getTime();
113	>	}
114	>	if (simParams->getUseRNEMD()){
115	>	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
116	>	}
117		needPotential = false;
118		needStress = false;
119	<
120	<	}
121	<
122	<	void VelocityVerletIntegrator::doIntegrate() {
123	<
111	<
119	>
120	>	}
121	>
122	>	void VelocityVerletIntegrator::doIntegrate() {
123	>
124		initialize();
125	+
126	+	while (currentSnapshot_->getTime() < runTime) {
127	+	preStep();
128	+	integrateStep();
129	+	postStep();
130	+	}
131	+	finalize();
132	+	}
133
114	–	while (currentSnapshot_->getTime() < runTime) {
115	–
116	–	preStep();
134
135	<	integrateStep();
136	<
137	<	postStep();
138	<
135	>	void VelocityVerletIntegrator::preStep() {
136	>	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
137	>
138	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
139	>	needPotential = true;
140	>	needStress = true;
141		}
142	+	}
143
144	<	finalize();
144	>	void VelocityVerletIntegrator::postStep() {
145	>
146	>	//save snapshot
147	>	info_->getSnapshotManager()->advance();
148	>
149	>	//increase time
150	>	currentSnapshot_->increaseTime(dt);
151	>
152	>	if (needVelocityScaling) {
153	>	if (currentSnapshot_->getTime() >= currThermal) {
154	>	velocitizer_->velocitize(targetScalingTemp);
155	>	currThermal += thermalTime;
156	>	}
157	>	}
158	>	if (useRNEMD) {
159	>	if (currentSnapshot_->getTime() >= currRNEMD) {
160	>	rnemd_->doRNEMD();
161	>	currRNEMD += RNEMD_exchangeTime;
162	>	}
163	>	rnemd_->collectData();
164	>	}
165
166	<	}
166	>	if (currentSnapshot_->getTime() >= currSample) {
167	>	dumpWriter->writeDumpAndEor();
168	>
169	>	currSample += sampleTime;
170	>	}
171	>
172	>	if (currentSnapshot_->getTime() >= currStatus) {
173	>	//save statistics, before writeStat,  we must save statistics
174	>	thermo.saveStat();
175	>	saveConservedQuantity();
176
177	+	if (simParams->getUseRNEMD()) {
178	+	rnemd_->getStatus();
179	+	}
180
181	<	void VelocityVerletIntegrator::preStep() {
130	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
181	>	statWriter->writeStat(currentSnapshot_->statData);
182
183	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
184	<	needPotential = true;
134	<	needStress = true;
135	<	}
183	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
184	>	progressBar->update();
185
186	<	}
186	>	needPotential = false;
187	>	needStress = false;
188	>	currStatus += statusTime;
189	>	}
190	>
191	>	if (needReset && currentSnapshot_->getTime() >= currReset) {
192	>	resetIntegrator();
193	>	currReset += resetTime;
194	>	}
195	>	}
196
139	–	void VelocityVerletIntegrator::postStep() {
197
198	<	//save snapshot
199	<	info_->getSnapshotManager()->advance();
200	<
144	<	//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	<
198	>	void VelocityVerletIntegrator::finalize() {
199	>	dumpWriter->writeEor();
200	>
201		delete dumpWriter;
181	–	delete eorWriter;
202		delete statWriter;
203	<
203	>
204		dumpWriter = NULL;
185	–	eorWriter = NULL;
205		statWriter = NULL;
206	<
188	<	}
206	>	}
207
208	<	void VelocityVerletIntegrator::integrateStep() {
209	<
208	>	void VelocityVerletIntegrator::integrateStep() {
209	>
210		moveA();
211	<	calcForce(needPotential, needStress);
211	>	calcForce();
212		moveB();
213	<	}
213	>	}
214
215
216	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
217	<	bool needStress) {
218	<	forceMan_->calcForces(needPotential, needStress);
219	<	}
216	>	void VelocityVerletIntegrator::calcForce() {
217	>	forceMan_->calcForces();
218	>	flucQ_->applyConstraints();
219	>	}
220
221	<	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
222	<	return new DumpWriter(info_, info_->getDumpFileName());
223	<	}
221	>	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
222	>	return new DumpWriter(info_);
223	>	}
224
225	<	DumpWriter* VelocityVerletIntegrator::createEorWriter() {
208	<	return new DumpWriter(info_, getPrefix(info_->getDumpFileName()) + ".eor");
209	<	}
225	>	StatWriter* VelocityVerletIntegrator::createStatWriter() {
226
227	<	StatWriter* VelocityVerletIntegrator::createStatWriter() {
228	<	return new StatWriter(info_->getStatFileName());
229	<	}
227	>	std::string statFileFormatString = simParams->getStatFileFormat();
228	>	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
229	>
230	>	// if we're doing a thermodynamic integration, we'll want the raw
231	>	// potential as well as the full potential:
232
233	+
234	+	if (simParams->getUseThermodynamicIntegration())
235	+	mask.set(Stats::VRAW);
236
237	<	} //end namespace oopse
237	>	// if we've got restraints turned on, we'll also want a report of the
238	>	// total harmonic restraints
239	>	if (simParams->getUseRestraints()){
240	>	mask.set(Stats::VHARM);
241	>	}
242	>
243	>	if (simParams->havePrintPressureTensor() &&
244	>	simParams->getPrintPressureTensor()){
245	>	mask.set(Stats::PRESSURE_TENSOR_XX);
246	>	mask.set(Stats::PRESSURE_TENSOR_XY);
247	>	mask.set(Stats::PRESSURE_TENSOR_XZ);
248	>	mask.set(Stats::PRESSURE_TENSOR_YX);
249	>	mask.set(Stats::PRESSURE_TENSOR_YY);
250	>	mask.set(Stats::PRESSURE_TENSOR_YZ);
251	>	mask.set(Stats::PRESSURE_TENSOR_ZX);
252	>	mask.set(Stats::PRESSURE_TENSOR_ZY);
253	>	mask.set(Stats::PRESSURE_TENSOR_ZZ);
254	>	}
255	>
256	>	if (simParams->getAccumulateBoxDipole()) {
257	>	mask.set(Stats::BOX_DIPOLE_X);
258	>	mask.set(Stats::BOX_DIPOLE_Y);
259	>	mask.set(Stats::BOX_DIPOLE_Z);
260	>	}
261	>
262	>	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
263	>	if (simParams->getPrintTaggedPairDistance()) {
264	>	mask.set(Stats::TAGGED_PAIR_DISTANCE);
265	>	}
266	>	}
267	>
268	>	if (simParams->getUseRNEMD()) {
269	>	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
270	>	}
271	>
272	>
273	>	return new StatWriter(info_->getStatFileName(), mask);
274	>	}
275	>
276	>
277	>	} //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 1718 by gezelter, Thu May 24 01:29:59 2012 UTC

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