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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 1878 by gezelter, Thu Jun 13 14:26:09 2013 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, 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) {
#	Line 89 | Line 91 | namespace oopse {
91		dumpWriter = createDumpWriter();
92
93		statWriter = createStatWriter();
94	<
93	<	if (simParams->getUseSolidThermInt()) {
94	<	restWriter = createRestWriter();
95	<	restWriter->writeZangle();
96	<	}
97	<
94	>
95		dumpWriter->writeDumpAndEor();
96	<
97	<
96	>
97	>	progressBar = new ProgressBar();
98	>
99		//save statistics, before writeStat,  we must save statistics
102	–	thermo.saveStat();
100		saveConservedQuantity();
101	<	statWriter->writeStat(currentSnapshot_->statData);
101	>	stats->collectStats();
102	>
103	>	if (simParams->getRNEMDParameters()->getUseRNEMD())
104	>	rnemd_->getStarted();
105	>
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->getRNEMDParameters()->getUseRNEMD()){
115	+	currRNEMD = RNEMD_exchangeTime + snap->getTime();
116	+	}
117		needPotential = false;
118		needStress = false;
119
120		}
121	<
121	>
122		void VelocityVerletIntegrator::doIntegrate() {
123
119	–
124		initialize();
125
126	<	while (currentSnapshot_->getTime() < runTime) {
127	<
128	<	preStep();
129	<
130	<	integrateStep();
127	<
128	<	postStep();
129	<
130	<	}
131	<
126	>	while (snap->getTime() < runTime) {
127	>	preStep();
128	>	integrateStep();
129	>	postStep();
130	>	}
131		finalize();
133	–
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) < oopse::epsilon) {
138	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
139		needPotential = true;
140		needStress = true;
141		}
#	Line 145 | Line 143 | namespace oopse {
143
144		void VelocityVerletIntegrator::postStep() {
145
146	<	//save snapshot
149	<	info_->getSnapshotManager()->advance();
150	<
151	<	//increase time
152	<	currentSnapshot_->increaseTime(dt);
153	<
146	>
147		if (needVelocityScaling) {
148	<	if (currentSnapshot_->getTime() >= currThermal) {
148	>	if (snap->getTime() >= currThermal) {
149		velocitizer_->velocitize(targetScalingTemp);
150		currThermal += thermalTime;
151		}
152		}
153	<
154	<	if (currentSnapshot_->getTime() >= currSample) {
155	<	dumpWriter->writeDumpAndEor();
153	>	if (useRNEMD) {
154	>	if (snap->getTime() >= currRNEMD) {
155	>	rnemd_->doRNEMD();
156	>	currRNEMD += RNEMD_exchangeTime;
157	>	}
158	>	rnemd_->collectData();
159	>	}
160
161	<	if (simParams->getUseSolidThermInt())
162	<	restWriter->writeZangle();
163	<
161	>	if (snap->getTime() >= currSample) {
162	>	dumpWriter->writeDumpAndEor();
163	>
164		currSample += sampleTime;
165		}
166	<
167	<	if (currentSnapshot_->getTime() >= currStatus) {
166	>
167	>	if (snap->getTime() >= currStatus) {
168		//save statistics, before writeStat,  we must save statistics
172	–	thermo.saveStat();
169		saveConservedQuantity();
170	<	statWriter->writeStat(currentSnapshot_->statData);
171	<
170	>	stats->collectStats();
171	>
172	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173	>	rnemd_->writeOutputFile();
174	>	}
175	>
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) {
187	<	resetIntegrator();
188	<	currReset += resetTime;
189	<	}
185	>
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	<
202	<	if (simParams->getUseSolidThermInt()) {
193	<	restWriter->writeZangle();
194	<	delete restWriter;
195	<	restWriter = NULL;
201	>	if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202	>	rnemd_->writeOutputFile();
203		}
204	<
204	>
205		delete dumpWriter;
206		delete statWriter;
207
208		dumpWriter = NULL;
209		statWriter = NULL;
203	–
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 221 | Line 227 | namespace oopse {
227		}
228
229		StatWriter* VelocityVerletIntegrator::createStatWriter() {
224	–
225	–	std::string statFileFormatString = simParams->getStatFileFormat();
226	–	StatsBitSet mask = parseStatFileFormat(statFileFormatString);
230
231	<	// if solidThermInt is true, add extra information to the statfile
232	<	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	<	}
231	>	stats = new Stats(info_);
232	>	statWriter = new StatWriter(info_->getStatFileName(), stats);
233
234	<	return new StatWriter(info_->getStatFileName(), mask);
234	>	return statWriter;
235		}
236
237	<	RestWriter* VelocityVerletIntegrator::createRestWriter(){
244	<	return new RestWriter(info_);
245	<	}
246	<
247	<
248	<	} //end namespace oopse
237	>	} //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 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

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