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Comparing branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1773 by gezelter, Tue Aug 7 18:26:40 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 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 124 | 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 144 | Line 143 | namespace OpenMD {
143  
144    void VelocityVerletIntegrator::postStep() {
145  
147 –    //save snapshot
148 –    info_->getSnapshotManager()->advance();
149 –  
150 –    //increase time
151 –    snap->increaseTime(dt);        
146    
147      if (needVelocityScaling) {
148        if (snap->getTime() >= currThermal) {
# Line 172 | Line 166 | namespace OpenMD {
166      
167      if (snap->getTime() >= currStatus) {
168        //save statistics, before writeStat,  we must save statistics
175 –      stats->collectStats();
169        saveConservedQuantity();
170 +      stats->collectStats();
171  
172        if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173          rnemd_->writeOutputFile();
# Line 193 | 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  
199    void VelocityVerletIntegrator::finalize() {
200      dumpWriter->writeEor();
201 <    rnemd_->writeOutputFile();
202 <  
201 >    if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202 >      rnemd_->writeOutputFile();
203 >    }
204 >
205      delete dumpWriter;
206      delete statWriter;
207    

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