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

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 50 | Line 50
50		#include "integrators/VelocityVerletIntegrator.hpp"
51		#include "integrators/DLM.hpp"
52		#include "utils/StringUtils.hpp"
53	+	#include "utils/ProgressBar.hpp"
54
55	<	namespace oopse {
55	>	namespace OpenMD {
56		VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
57		dt2 = 0.5 * dt;
58		rotAlgo = new DLM();
#	Line 72 | Line 73 | namespace oopse {
73		velocitizer_->removeComDrift();
74
75		// initialize the forces before the first step
76	<	calcForce(true, true);
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);
82	>	calcForce();
83		rattle->constraintB();
84		//copy the current snapshot to previous snapshot
85		info_->getSnapshotManager()->advance();
#	Line 94 | Line 95 | namespace oopse {
95
96		dumpWriter->writeDumpAndEor();
97
98	<	if (simParams->getUseSolidThermInt()) {
99	<	restWriter = createRestWriter();
99	<	restWriter->writeZAngFile();
100	<	}
101	<
98	>	progressBar = new ProgressBar();
99	>
100		//save statistics, before writeStat,  we must save statistics
101		thermo.saveStat();
102		saveConservedQuantity();
103		if (simParams->getUseRNEMD())
104	<	rnemd_->getStatus();
104	>	rnemd_->getStarted();
105
106		statWriter->writeStat(currentSnapshot_->statData);
107
#	Line 114 | Line 112 | namespace oopse {
112		currReset = resetTime + currentSnapshot_->getTime();
113		}
114		if (simParams->getUseRNEMD()){
115	<	currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
115	>	currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
116		}
117		needPotential = false;
118		needStress = false;
119
120		}
121	<
121	>
122		void VelocityVerletIntegrator::doIntegrate() {
123
124
#	Line 133 | Line 131 | namespace oopse {
131		integrateStep();
132
133		postStep();
134	<
134	>
135		}
136
137		finalize();
#	Line 144 | Line 142 | namespace oopse {
142		void VelocityVerletIntegrator::preStep() {
143		RealType difference = currentSnapshot_->getTime() + dt - currStatus;
144
145	<	if (difference > 0 || fabs(difference) < oopse::epsilon) {
145	>	if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
146		needPotential = true;
147		needStress = true;
148		}
#	Line 166 | Line 164 | namespace oopse {
164		}
165		if (useRNEMD) {
166		if (currentSnapshot_->getTime() >= currRNEMD) {
167	<	rnemd_->doSwap();
168	<	currRNEMD += RNEMD_swapTime;
167	>	rnemd_->doRNEMD();
168	>	currRNEMD += RNEMD_exchangeTime;
169		}
170	+	rnemd_->collectData();
171		}
172
173		if (currentSnapshot_->getTime() >= currSample) {
174		dumpWriter->writeDumpAndEor();
176	–
177	–	if (simParams->getUseSolidThermInt())
178	–	restWriter->writeZAngFile();
175
176		currSample += sampleTime;
177		}
#	Line 185 | Line 181 | namespace oopse {
181		thermo.saveStat();
182		saveConservedQuantity();
183
184	<	if (simParams->getUseRNEMD())
184	>	if (simParams->getUseRNEMD()) {
185		rnemd_->getStatus();
186	+	}
187
188		statWriter->writeStat(currentSnapshot_->statData);
189	<
189	>
190	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
191	>	progressBar->update();
192	>
193		needPotential = false;
194		needStress = false;
195		currStatus += statusTime;
#	Line 205 | Line 205 | namespace oopse {
205		void VelocityVerletIntegrator::finalize() {
206		dumpWriter->writeEor();
207
208	–	if (simParams->getUseSolidThermInt()) {
209	–	restWriter->writeZAngFile();
210	–	delete restWriter;
211	–	restWriter = NULL;
212	–	}
213	–
208		delete dumpWriter;
209		delete statWriter;
210
#	Line 222 | Line 216 | namespace oopse {
216		void VelocityVerletIntegrator::integrateStep() {
217
218		moveA();
219	<	calcForce(needPotential, needStress);
219	>	calcForce();
220		moveB();
221		}
222
223
224	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
225	<	bool needStress) {
232	<	forceMan_->calcForces(needPotential, needStress);
224	>	void VelocityVerletIntegrator::calcForce() {
225	>	forceMan_->calcForces();
226		}
227
228		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
#	Line 240 | Line 233 | namespace oopse {
233
234		std::string statFileFormatString = simParams->getStatFileFormat();
235		StatsBitSet mask = parseStatFileFormat(statFileFormatString);
236	<
237	<	// if solidThermInt is true, add extra information to the statfile
238	<	if (simParams->getUseSolidThermInt()){
236	>
237	>	// if we're doing a thermodynamic integration, we'll want the raw
238	>	// potential as well as the full potential:
239	>
240	>
241	>	if (simParams->getUseThermodynamicIntegration())
242		mask.set(Stats::VRAW);
243	+
244	+	// if we've got restraints turned on, we'll also want a report of the
245	+	// total harmonic restraints
246	+	if (simParams->getUseRestraints()){
247		mask.set(Stats::VHARM);
248		}
249
#	Line 273 | Line 273 | namespace oopse {
273		}
274
275		if (simParams->getUseRNEMD()) {
276	<	mask.set(Stats::RNEMD_SWAP_TOTAL);
276	>	mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
277		}
278	<
278	>
279
280	<	return new StatWriter(info_->getStatFileName(), mask);
280	>	return new StatWriter(info_->getStatFileName(), mask);
281		}
282
283	–	RestWriter* VelocityVerletIntegrator::createRestWriter(){
284	–	return new RestWriter(info_);
285	–	}
283
284	<
288	<	} //end namespace oopse
284	>	} //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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