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root/OpenMD/trunk/src/integrators/VelocityVerletIntegrator.cpp
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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1915 by gezelter, Mon Jul 29 17:55:17 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 44 | Line 44
44   * @file VelocityVerletIntegrator.cpp
45   * @author tlin
46   * @date 11/09/2004
47 – * @time 16:16am
47   * @version 1.0
48   */
49  
# Line 89 | Line 88 | namespace OpenMD {
88        velocitizer_->velocitize(targetScalingTemp);
89      }
90      
91 <    dumpWriter = createDumpWriter();
92 <    
94 <    statWriter = createStatWriter();
95 <
91 >    dumpWriter = createDumpWriter();    
92 >    statWriter = createStatWriter();
93      dumpWriter->writeDumpAndEor();
94  
95      progressBar = new ProgressBar();
# Line 124 | Line 121 | namespace OpenMD {
121    
122      initialize();
123    
124 <    while (snap->getTime() < runTime) {    
124 >    while (snap->getTime() < runTime) {
125        preStep();    
126        integrateStep();    
127        postStep();      
# Line 144 | Line 141 | namespace OpenMD {
141  
142    void VelocityVerletIntegrator::postStep() {
143  
147 –    //save snapshot
148 –    info_->getSnapshotManager()->advance();
149 –  
150 –    //increase time
151 –    snap->increaseTime(dt);        
144    
145      if (needVelocityScaling) {
146        if (snap->getTime() >= currThermal) {
# Line 172 | Line 164 | namespace OpenMD {
164      
165      if (snap->getTime() >= currStatus) {
166        //save statistics, before writeStat,  we must save statistics
175 –      stats->collectStats();
167        saveConservedQuantity();
168 +      stats->collectStats();
169  
170        if (simParams->getRNEMDParameters()->getUseRNEMD()) {
171          rnemd_->writeOutputFile();
# Line 193 | Line 185 | namespace OpenMD {
185        resetIntegrator();
186        currReset += resetTime;
187      }        
188 +    //save snapshot
189 +    info_->getSnapshotManager()->advance();
190 +  
191 +    //increase time
192 +    snap->increaseTime(dt);        
193 +
194    }
195  
196  

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