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

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

#	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;
57	–	rotAlgo = new DLM();
58	–	rattle = new Rattle(info);
59		}
60
61		VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62	–	delete rotAlgo;
63	–	delete rattle;
62		}
63
64		void VelocityVerletIntegrator::initialize(){
65
66	<	forceMan_->init();
66	>	forceMan_->initialize();
67
68	<	// remove center of mass drift velocity (in case we passed in a configuration
69	<	// that was drifting
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);
76	>	calcForce();
77
78	<	//execute constraint algorithm to make sure at the very beginning the system is constrained
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
88		if (needVelocityScaling) {
#	Line 89 | Line 92 | namespace oopse {
92		dumpWriter = createDumpWriter();
93
94		statWriter = createStatWriter();
95	<
93	<	if (simParams->getUseSolidThermInt()) {
94	<	restWriter = createRestWriter();
95	<	restWriter->writeZangle();
96	<	}
97	<
95	>
96		dumpWriter->writeDumpAndEor();
97	<
98	<
97	>
98	>	progressBar = new ProgressBar();
99	>
100		//save statistics, before writeStat,  we must save statistics
102	–	thermo.saveStat();
101		saveConservedQuantity();
102	<	statWriter->writeStat(currentSnapshot_->statData);
102	>	stats->collectStats();
103	>
104	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
105	>	rnemd_->getStarted();
106	>
107	>	statWriter->writeStat();
108
109	<	currSample = sampleTime + currentSnapshot_->getTime();
110	<	currStatus =  statusTime + currentSnapshot_->getTime();;
111	<	currThermal = thermalTime + currentSnapshot_->getTime();
109	>	currSample = sampleTime + snap->getTime();
110	>	currStatus =  statusTime + snap->getTime();
111	>	currThermal = thermalTime + snap->getTime();
112		if (needReset) {
113	<	currReset = resetTime + currentSnapshot_->getTime();
113	>	currReset = resetTime + snap->getTime();
114		}
115	+	if (simParams->getRNEMDParameters()->getUseRNEMD()){
116	+	currRNEMD = RNEMD_exchangeTime + snap->getTime();
117	+	}
118		needPotential = false;
119		needStress = false;
120
121		}
122	<
122	>
123		void VelocityVerletIntegrator::doIntegrate() {
124
119	–
125		initialize();
126
127	<	while (currentSnapshot_->getTime() < runTime) {
128	<
129	<	preStep();
130	<
131	<	integrateStep();
127	<
128	<	postStep();
129	<
130	<	}
131	<
127	>	while (snap->getTime() < runTime) {
128	>	preStep();
129	>	integrateStep();
130	>	postStep();
131	>	}
132		finalize();
133	–
133		}
134
135
136		void VelocityVerletIntegrator::preStep() {
137	<	RealType difference = currentSnapshot_->getTime() + dt - currStatus;
137	>	RealType difference = snap->getTime() + dt - currStatus;
138
139	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
139	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
140		needPotential = true;
141		needStress = true;
142		}
#	Line 149 | Line 148 | namespace oopse {
148		info_->getSnapshotManager()->advance();
149
150		//increase time
151	<	currentSnapshot_->increaseTime(dt);
152	<
151	>	snap->increaseTime(dt);
152	>
153		if (needVelocityScaling) {
154	<	if (currentSnapshot_->getTime() >= currThermal) {
154	>	if (snap->getTime() >= currThermal) {
155		velocitizer_->velocitize(targetScalingTemp);
156		currThermal += thermalTime;
157		}
158		}
159	<
160	<	if (currentSnapshot_->getTime() >= currSample) {
161	<	dumpWriter->writeDumpAndEor();
159	>	if (useRNEMD) {
160	>	if (snap->getTime() >= currRNEMD) {
161	>	rnemd_->doRNEMD();
162	>	currRNEMD += RNEMD_exchangeTime;
163	>	}
164	>	rnemd_->collectData();
165	>	}
166
167	<	if (simParams->getUseSolidThermInt())
168	<	restWriter->writeZangle();
169	<
167	>	if (snap->getTime() >= currSample) {
168	>	dumpWriter->writeDumpAndEor();
169	>
170		currSample += sampleTime;
171		}
172	<
173	<	if (currentSnapshot_->getTime() >= currStatus) {
172	>
173	>	if (snap->getTime() >= currStatus) {
174		//save statistics, before writeStat,  we must save statistics
175	<	thermo.saveStat();
175	>	stats->collectStats();
176		saveConservedQuantity();
177	<	statWriter->writeStat(currentSnapshot_->statData);
178	<
177	>
178	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
179	>	rnemd_->writeOutputFile();
180	>	}
181	>
182	>	statWriter->writeStat();
183	>
184	>	progressBar->setStatus(snap->getTime(), runTime);
185	>	progressBar->update();
186	>
187		needPotential = false;
188		needStress = false;
189		currStatus += statusTime;
190		}
191	<
192	<	if (needReset && currentSnapshot_->getTime() >= currReset) {
193	<	resetIntegrator();
194	<	currReset += resetTime;
195	<	}
185	<
191	>
192	>	if (needReset && snap->getTime() >= currReset) {
193	>	resetIntegrator();
194	>	currReset += resetTime;
195	>	}
196		}
197
198
199		void VelocityVerletIntegrator::finalize() {
200		dumpWriter->writeEor();
201	+	rnemd_->writeOutputFile();
202
192	–	if (simParams->getUseSolidThermInt()) {
193	–	restWriter->writeZangle();
194	–	delete restWriter;
195	–	restWriter = NULL;
196	–	}
197	–
203		delete dumpWriter;
204		delete statWriter;
205
206		dumpWriter = NULL;
207		statWriter = NULL;
203	–
208		}
209
210		void VelocityVerletIntegrator::integrateStep() {
211
212		moveA();
213	<	calcForce(needPotential, needStress);
213	>	calcForce();
214		moveB();
215		}
216
217
218	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
219	<	bool needStress) {
220	<	forceMan_->calcForces(needPotential, needStress);
218	>	void VelocityVerletIntegrator::calcForce() {
219	>	forceMan_->calcForces();
220	>	flucQ_->applyConstraints();
221		}
222
223		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
#	Line 221 | Line 225 | namespace oopse {
225		}
226
227		StatWriter* VelocityVerletIntegrator::createStatWriter() {
224	–
225	–	std::string statFileFormatString = simParams->getStatFileFormat();
226	–	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
228
229	<	// if solidThermInt is true, add extra information to the statfile
230	<	if (simParams->getUseSolidThermInt()){
230	<	mask.set(Stats::VRAW);
231	<	mask.set(Stats::VHARM);
232	<	}
233	<
234	<	if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
235	<	mask.set(Stats::PRESSURE_TENSOR_X);
236	<	mask.set(Stats::PRESSURE_TENSOR_Y);
237	<	mask.set(Stats::PRESSURE_TENSOR_Z);
238	<	}
229	>	stats = new Stats(info_);
230	>	statWriter = new StatWriter(info_->getStatFileName(), stats);
231
232	<	return new StatWriter(info_->getStatFileName(), mask);
232	>	return statWriter;
233		}
234
235	<	RestWriter* VelocityVerletIntegrator::createRestWriter(){
244	<	return new RestWriter(info_);
245	<	}
246	<
247	<
248	<	} //end namespace oopse
235	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1773 by gezelter, Tue Aug 7 18:26:40 2012 UTC

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