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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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 36 | Line 36
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).
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 OpenMD {
57		VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
#	Line 65 | Line 67 | namespace OpenMD {
67
68		void VelocityVerletIntegrator::initialize(){
69
70	<	forceMan_->init();
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
76		// initialize the forces before the first step
77	<	calcForce(true, true);
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);
83	>	calcForce();
84		rattle->constraintB();
85		//copy the current snapshot to previous snapshot
86		info_->getSnapshotManager()->advance();
#	Line 94 | Line 96 | namespace OpenMD {
96
97		dumpWriter->writeDumpAndEor();
98
99	+	progressBar = new ProgressBar();
100	+
101		//save statistics, before writeStat,  we must save statistics
102		thermo.saveStat();
103		saveConservedQuantity();
#	Line 115 | Line 119 | namespace OpenMD {
119		needStress = false;
120
121		}
122	<
122	>
123		void VelocityVerletIntegrator::doIntegrate() {
124
125
#	Line 128 | Line 132 | namespace OpenMD {
132		integrateStep();
133
134		postStep();
135	<
135	>
136		}
137
138		finalize();
#	Line 160 | Line 164 | namespace OpenMD {
164		}
165		}
166		if (useRNEMD) {
163	–	rnemd_->collectData();
167		if (currentSnapshot_->getTime() >= currRNEMD) {
168		rnemd_->doRNEMD();
169		currRNEMD += RNEMD_exchangeTime;
170		}
171	+	rnemd_->collectData();
172		}
173
174		if (currentSnapshot_->getTime() >= currSample) {
#	Line 183 | Line 187 | namespace OpenMD {
187		}
188
189		statWriter->writeStat(currentSnapshot_->statData);
190	<
190	>
191	>	progressBar->setStatus(currentSnapshot_->getTime(), runTime);
192	>	progressBar->update();
193	>
194		needPotential = false;
195		needStress = false;
196		currStatus += statusTime;
#	Line 210 | Line 217 | namespace OpenMD {
217		void VelocityVerletIntegrator::integrateStep() {
218
219		moveA();
220	<	calcForce(needPotential, needStress);
220	>	calcForce();
221		moveB();
222		}
223
224
225	<	void VelocityVerletIntegrator::calcForce(bool needPotential,
226	<	bool needStress) {
220	<	forceMan_->calcForces(needPotential, needStress);
225	>	void VelocityVerletIntegrator::calcForce() {
226	>	forceMan_->calcForces();
227		}
228
229		DumpWriter* VelocityVerletIntegrator::createDumpWriter() {

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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

#	Line 0 | Line 1
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