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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 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), rotAlgo(NULL) {
58		dt2 = 0.5 * dt;
59		rotAlgo = new DLM();
60		rattle = new Rattle(info);
61	<	}
62	<
63	<	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
61	>	}
62	>
63	>	VelocityVerletIntegrator::~VelocityVerletIntegrator() {
64		delete rotAlgo;
65		delete rattle;
66	<	}
67	<
68	<	void VelocityVerletIntegrator::initialize(){
69	<
70	<	forceMan_->init();
71	<
72	<	// remove center of mass drift velocity (in case we passed in a configuration
73	<	// that was drifting
66	>	}
67	>
68	>	void VelocityVerletIntegrator::initialize(){
69	>
70	>	forceMan_->initialize();
71	>
72	>	// remove center of mass drift velocity (in case we passed in a
73	>	// configuration that was drifting)
74		velocitizer_->removeComDrift();
75	<
75	>
76		// initialize the forces before the first step
77	<	calcForce(true, true);
78	<
79	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
77	>	calcForce();
78	>
79	>	// execute the constraint algorithm to make sure that the system is
80	>	// constrained at the very beginning
81		if (info_->getNGlobalConstraints() > 0) {
82	<	rattle->constraintA();
83	<	calcForce(true, true);
84	<	rattle->constraintB();
85	<	info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
82	>	rattle->constraintA();
83	>	calcForce();
84	>	rattle->constraintB();
85	>	//copy the current snapshot to previous snapshot
86	>	info_->getSnapshotManager()->advance();
87		}
88	<
88	>
89		if (needVelocityScaling) {
90	<	velocitizer_->velocitize(targetScalingTemp);
90	>	velocitizer_->velocitize(targetScalingTemp);
91		}
92
93		dumpWriter = createDumpWriter();
94	<	eorWriter = createEorWriter();
94	>
95		statWriter = createStatWriter();
96	+
97	+	dumpWriter->writeDumpAndEor();
98
99	<	dumpWriter->writeDump();
100	<	eorWriter->writeDump();
95	<
99	>	progressBar = new ProgressBar();
100	>
101		//save statistics, before writeStat,  we must save statistics
102		thermo.saveStat();
103		saveConservedQuantity();
104	<	statWriter->writeStat(currentSnapshot_->statData);
104	>	if (simParams->getUseRNEMD())
105	>	rnemd_->getStarted();
106
107	+	statWriter->writeStat(currentSnapshot_->statData);
108	+
109		currSample = sampleTime + currentSnapshot_->getTime();
110	<	currStatus =  statusTime + currentSnapshot_->getTime();;
111	<	currThermal = thermalTime +  + currentSnapshot_->getTime();
110	>	currStatus =  statusTime + currentSnapshot_->getTime();
111	>	currThermal = thermalTime + currentSnapshot_->getTime();
112	>	if (needReset) {
113	>	currReset = resetTime + currentSnapshot_->getTime();
114	>	}
115	>	if (simParams->getUseRNEMD()){
116	>	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
117	>	}
118		needPotential = false;
119		needStress = false;
120	<
121	<	}
122	<
123	<	void VelocityVerletIntegrator::doIntegrate() {
124	<
125	<
120	>
121	>	}
122	>
123	>	void VelocityVerletIntegrator::doIntegrate() {
124	>
125	>
126		initialize();
127	<
127	>
128		while (currentSnapshot_->getTime() < runTime) {
129	<
130	<	preStep();
131	<
132	<	integrateStep();
133	<
134	<	postStep();
135	<
129	>
130	>	preStep();
131	>
132	>	integrateStep();
133	>
134	>	postStep();
135	>
136		}
137	<
137	>
138		finalize();
139	<
140	<	}
139	>
140	>	}
141
142
143	<	void VelocityVerletIntegrator::preStep() {
144	<	double difference = currentSnapshot_->getTime() + dt - currStatus;
143	>	void VelocityVerletIntegrator::preStep() {
144	>	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
145	>
146	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
147	>	needPotential = true;
148	>	needStress = true;
149	>	}
150	>	}
151
152	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
133	<	needPotential = true;
134	<	needStress = true;
135	<	}
152	>	void VelocityVerletIntegrator::postStep() {
153
154	<	}
154	>	//save snapshot
155	>	info_->getSnapshotManager()->advance();
156	>
157	>	//increase time
158	>	currentSnapshot_->increaseTime(dt);
159	>
160	>	if (needVelocityScaling) {
161	>	if (currentSnapshot_->getTime() >= currThermal) {
162	>	velocitizer_->velocitize(targetScalingTemp);
163	>	currThermal += thermalTime;
164	>	}
165	>	}
166	>	if (useRNEMD) {
167	>	if (currentSnapshot_->getTime() >= currRNEMD) {
168	>	rnemd_->doRNEMD();
169	>	currRNEMD += RNEMD_exchangeTime;
170	>	}
171	>	rnemd_->collectData();
172	>	}
173	>
174	>	if (currentSnapshot_->getTime() >= currSample) {
175	>	dumpWriter->writeDumpAndEor();
176	>
177	>	currSample += sampleTime;
178	>	}
179	>
180	>	if (currentSnapshot_->getTime() >= currStatus) {
181	>	//save statistics, before writeStat,  we must save statistics
182	>	thermo.saveStat();
183	>	saveConservedQuantity();
184
185	<	void VelocityVerletIntegrator::postStep() {
185	>	if (simParams->getUseRNEMD()) {
186	>	rnemd_->getStatus();
187	>	}
188
189	<	//save snapshot
142	<	info_->getSnapshotManager()->advance();
189	>	statWriter->writeStat(currentSnapshot_->statData);
190
191	<	//increase time
192	<	currentSnapshot_->increaseTime(dt);
146	<
147	<	if (needVelocityScaling) {
148	<	if (currentSnapshot_->getTime() >= currThermal) {
149	<	velocitizer_->velocitize(targetScalingTemp);
150	<	currThermal += thermalTime;
151	<	}
152	<	}
191	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
192	>	progressBar->update();
193
194	<	if (currentSnapshot_->getTime() >= currSample) {
195	<	dumpWriter->writeDump();
196	<	eorWriter->writeDump();
197	<	currSample += sampleTime;
198	<	}
194	>	needPotential = false;
195	>	needStress = false;
196	>	currStatus += statusTime;
197	>	}
198	>
199	>	if (needReset && currentSnapshot_->getTime() >= currReset) {
200	>	resetIntegrator();
201	>	currReset += resetTime;
202	>	}
203	>	}
204
160	–	if (currentSnapshot_->getTime() >= currStatus) {
161	–	//save statistics, before writeStat,  we must save statistics
162	–	thermo.saveStat();
163	–	saveConservedQuantity();
164	–	statWriter->writeStat(currentSnapshot_->statData);
205
206	<	needPotential = false;
207	<	needStress = false;
208	<	currStatus += statusTime;
169	<	}
170	<
171	<
172	<	}
173	<
174	<
175	<	void VelocityVerletIntegrator::finalize() {
176	<
177	<	dumpWriter->writeDump();
178	<	eorWriter->writeDump();
179	<
206	>	void VelocityVerletIntegrator::finalize() {
207	>	dumpWriter->writeEor();
208	>
209		delete dumpWriter;
181	–	delete eorWriter;
210		delete statWriter;
211	<
211	>
212		dumpWriter = NULL;
185	–	eorWriter = NULL;
213		statWriter = NULL;
214	<
215	<	}
214	>
215	>	}
216
217	<	void VelocityVerletIntegrator::integrateStep() {
218	<
217	>	void VelocityVerletIntegrator::integrateStep() {
218	>
219		moveA();
220	<	calcForce(needPotential, needStress);
220	>	calcForce();
221		moveB();
222	<	}
222	>	}
223
224
225	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
226	<	bool needStress) {
227	<	forceMan_->calcForces(needPotential, needStress);
201	<	}
225	>	void VelocityVerletIntegrator::calcForce() {
226	>	forceMan_->calcForces();
227	>	}
228
229	<	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
230	<	return new DumpWriter(info_, info_->getDumpFileName());
231	<	}
229	>	DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
230	>	return new DumpWriter(info_);
231	>	}
232
233	<	DumpWriter* VelocityVerletIntegrator::createEorWriter() {
208	<	return new DumpWriter(info_, getPrefix(info_->getDumpFileName()) + ".eor");
209	<	}
233	>	StatWriter* VelocityVerletIntegrator::createStatWriter() {
234
235	<	StatWriter* VelocityVerletIntegrator::createStatWriter() {
236	<	return new StatWriter(info_->getStatFileName());
237	<	}
235	>	std::string statFileFormatString = simParams->getStatFileFormat();
236	>	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
237	>
238	>	// if we're doing a thermodynamic integration, we'll want the raw
239	>	// potential as well as the full potential:
240
241	+
242	+	if (simParams->getUseThermodynamicIntegration())
243	+	mask.set(Stats::VRAW);
244
245	<	} //end namespace oopse
245	>	// if we've got restraints turned on, we'll also want a report of the
246	>	// total harmonic restraints
247	>	if (simParams->getUseRestraints()){
248	>	mask.set(Stats::VHARM);
249	>	}
250	>
251	>	if (simParams->havePrintPressureTensor() &&
252	>	simParams->getPrintPressureTensor()){
253	>	mask.set(Stats::PRESSURE_TENSOR_XX);
254	>	mask.set(Stats::PRESSURE_TENSOR_XY);
255	>	mask.set(Stats::PRESSURE_TENSOR_XZ);
256	>	mask.set(Stats::PRESSURE_TENSOR_YX);
257	>	mask.set(Stats::PRESSURE_TENSOR_YY);
258	>	mask.set(Stats::PRESSURE_TENSOR_YZ);
259	>	mask.set(Stats::PRESSURE_TENSOR_ZX);
260	>	mask.set(Stats::PRESSURE_TENSOR_ZY);
261	>	mask.set(Stats::PRESSURE_TENSOR_ZZ);
262	>	}
263	>
264	>	if (simParams->getAccumulateBoxDipole()) {
265	>	mask.set(Stats::BOX_DIPOLE_X);
266	>	mask.set(Stats::BOX_DIPOLE_Y);
267	>	mask.set(Stats::BOX_DIPOLE_Z);
268	>	}
269	>
270	>	if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
271	>	if (simParams->getPrintTaggedPairDistance()) {
272	>	mask.set(Stats::TAGGED_PAIR_DISTANCE);
273	>	}
274	>	}
275	>
276	>	if (simParams->getUseRNEMD()) {
277	>	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
278	>	}
279	>
280	>
281	>	return new StatWriter(info_->getStatFileName(), mask);
282	>	}
283	>
284	>
285	>	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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