[ViewVC] Diff of: OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.cpp

Comparing branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC vs.
Revision 1878 by gezelter, Thu Jun 13 14:26:09 2013 UTC

#	Line 35 \| Line 35
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).
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		*/
#	Line 123 \| Line 123 \| namespace OpenMD {
123
124		initialize();
125
126	<	while (snap->getTime() < runTime) {
126	>	while (snap->getTime() < runTime) {
127		preStep();
128		integrateStep();
129		postStep();
#	Line 143 \| Line 143 \| namespace OpenMD {
143
144		void VelocityVerletIntegrator::postStep() {
145
146	–	//save snapshot
147	–	info_->getSnapshotManager()->advance();
148	–
149	–	//increase time
150	–	snap->increaseTime(dt);
146
147		if (needVelocityScaling) {
148		if (snap->getTime() >= currThermal) {
#	Line 171 \| Line 166 \| namespace OpenMD {
166
167		if (snap->getTime() >= currStatus) {
168		//save statistics, before writeStat, we must save statistics
174	–	stats->collectStats();
169		saveConservedQuantity();
170	+	stats->collectStats();
171
172		if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173		rnemd_->writeOutputFile();
#	Line 192 \| Line 187 \| namespace OpenMD {
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

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