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

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

#	Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).
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 OpenMD {
56	<	VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
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
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 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();
80	>	rattle_->constraintA();
81	>	calcForce();
82	>	rattle_->constraintB();
83		//copy the current snapshot to previous snapshot
84		info_->getSnapshotManager()->advance();
85		}
#	Line 94 | Line 94 | namespace OpenMD {
94
95		dumpWriter->writeDumpAndEor();
96
97	+	progressBar = new ProgressBar();
98	+
99		//save statistics, before writeStat,  we must save statistics
98	–	thermo.saveStat();
100		saveConservedQuantity();
101	<	if (simParams->getUseRNEMD())
101	>	stats->collectStats();
102	>
103	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
104		rnemd_->getStarted();
105
106	<	statWriter->writeStat(currentSnapshot_->statData);
106	>	statWriter->writeStat();
107
108	<	currSample = sampleTime + currentSnapshot_->getTime();
109	<	currStatus =  statusTime + currentSnapshot_->getTime();
110	<	currThermal = thermalTime + currentSnapshot_->getTime();
108	>	currSample = sampleTime + snap->getTime();
109	>	currStatus =  statusTime + snap->getTime();
110	>	currThermal = thermalTime + snap->getTime();
111		if (needReset) {
112	<	currReset = resetTime + currentSnapshot_->getTime();
112	>	currReset = resetTime + snap->getTime();
113		}
114	<	if (simParams->getUseRNEMD()){
115	<	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
114	>	if (simParams->getRNEMDParameters()->getUseRNEMD()){
115	>	currRNEMD = RNEMD_exchangeTime + snap->getTime();
116		}
117		needPotential = false;
118		needStress = false;
119
120		}
121	<
121	>
122		void VelocityVerletIntegrator::doIntegrate() {
123
121	–
124		initialize();
125
126	<	while (currentSnapshot_->getTime() < runTime) {
127	<
128	<	preStep();
129	<
130	<	integrateStep();
129	<
130	<	postStep();
131	<
132	<	}
133	<
126	>	while (snap->getTime() < runTime) {
127	>	preStep();
128	>	integrateStep();
129	>	postStep();
130	>	}
131		finalize();
135	–
132		}
133
134
135		void VelocityVerletIntegrator::preStep() {
136	<	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
136	>	RealType difference = snap->getTime() + dt - currStatus;
137
138		if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
139		needPotential = true;
#	Line 147 | Line 143 | namespace OpenMD {
143
144		void VelocityVerletIntegrator::postStep() {
145
150	–	//save snapshot
151	–	info_->getSnapshotManager()->advance();
152	–
153	–	//increase time
154	–	currentSnapshot_->increaseTime(dt);
146
147		if (needVelocityScaling) {
148	<	if (currentSnapshot_->getTime() >= currThermal) {
148	>	if (snap->getTime() >= currThermal) {
149		velocitizer_->velocitize(targetScalingTemp);
150		currThermal += thermalTime;
151		}
152		}
153		if (useRNEMD) {
154	<	rnemd_->collectData();
164	<	if (currentSnapshot_->getTime() >= currRNEMD) {
154	>	if (snap->getTime() >= currRNEMD) {
155		rnemd_->doRNEMD();
156		currRNEMD += RNEMD_exchangeTime;
157		}
158	+	rnemd_->collectData();
159		}
160
161	<	if (currentSnapshot_->getTime() >= currSample) {
161	>	if (snap->getTime() >= currSample) {
162		dumpWriter->writeDumpAndEor();
163
164		currSample += sampleTime;
165		}
166
167	<	if (currentSnapshot_->getTime() >= currStatus) {
167	>	if (snap->getTime() >= currStatus) {
168		//save statistics, before writeStat,  we must save statistics
178	–	thermo.saveStat();
169		saveConservedQuantity();
170	<
171	<	if (simParams->getUseRNEMD()) {
172	<	rnemd_->getStatus();
170	>	stats->collectStats();
171	>
172	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173	>	rnemd_->writeOutputFile();
174		}
175
176	<	statWriter->writeStat(currentSnapshot_->statData);
177	<
176	>	statWriter->writeStat();
177	>
178	>	progressBar->setStatus(snap->getTime(), runTime);
179	>	progressBar->update();
180	>
181		needPotential = false;
182		needStress = false;
183		currStatus += statusTime;
184		}
185
186	<	if (needReset && currentSnapshot_->getTime() >= currReset) {
186	>	if (needReset && snap->getTime() >= currReset) {
187		resetIntegrator();
188		currReset += resetTime;
189		}
190	+	//save snapshot
191	+	info_->getSnapshotManager()->advance();
192	+
193	+	//increase time
194	+	snap->increaseTime(dt);
195	+
196		}
197
198
199		void VelocityVerletIntegrator::finalize() {
200		dumpWriter->writeEor();
201	<
201	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202	>	rnemd_->writeOutputFile();
203	>	}
204	>
205		delete dumpWriter;
206		delete statWriter;
207
208		dumpWriter = NULL;
209		statWriter = NULL;
207	–
210		}
211
212		void VelocityVerletIntegrator::integrateStep() {
213
214		moveA();
215	<	calcForce(needPotential, needStress);
215	>	calcForce();
216		moveB();
217		}
218
219
220	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
221	<	bool needStress) {
222	<	forceMan_->calcForces(needPotential, needStress);
220	>	void VelocityVerletIntegrator::calcForce() {
221	>	forceMan_->calcForces();
222	>	flucQ_->applyConstraints();
223		}
224
225		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
#	Line 225 | Line 227 | namespace OpenMD {
227		}
228
229		StatWriter* VelocityVerletIntegrator::createStatWriter() {
228	–
229	–	std::string statFileFormatString = simParams->getStatFileFormat();
230	–	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
231	–
232	–	// if we're doing a thermodynamic integration, we'll want the raw
233	–	// potential as well as the full potential:
234	–
235	–
236	–	if (simParams->getUseThermodynamicIntegration())
237	–	mask.set(Stats::VRAW);
238	–
239	–	// if we've got restraints turned on, we'll also want a report of the
240	–	// total harmonic restraints
241	–	if (simParams->getUseRestraints()){
242	–	mask.set(Stats::VHARM);
243	–	}
244	–
245	–	if (simParams->havePrintPressureTensor() &&
246	–	simParams->getPrintPressureTensor()){
247	–	mask.set(Stats::PRESSURE_TENSOR_XX);
248	–	mask.set(Stats::PRESSURE_TENSOR_XY);
249	–	mask.set(Stats::PRESSURE_TENSOR_XZ);
250	–	mask.set(Stats::PRESSURE_TENSOR_YX);
251	–	mask.set(Stats::PRESSURE_TENSOR_YY);
252	–	mask.set(Stats::PRESSURE_TENSOR_YZ);
253	–	mask.set(Stats::PRESSURE_TENSOR_ZX);
254	–	mask.set(Stats::PRESSURE_TENSOR_ZY);
255	–	mask.set(Stats::PRESSURE_TENSOR_ZZ);
256	–	}
230
231	<	if (simParams->getAccumulateBoxDipole()) {
232	<	mask.set(Stats::BOX_DIPOLE_X);
260	<	mask.set(Stats::BOX_DIPOLE_Y);
261	<	mask.set(Stats::BOX_DIPOLE_Z);
262	<	}
263	<
264	<	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
265	<	if (simParams->getPrintTaggedPairDistance()) {
266	<	mask.set(Stats::TAGGED_PAIR_DISTANCE);
267	<	}
268	<	}
269	<
270	<	if (simParams->getUseRNEMD()) {
271	<	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272	<	}
231	>	stats = new Stats(info_);
232	>	statWriter = new StatWriter(info_->getStatFileName(), stats);
233
234	<
275	<	return new StatWriter(info_->getStatFileName(), mask);
234	>	return statWriter;
235		}
236
278	–
237		} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

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