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root/OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.cpp
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Comparing branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1715 by gezelter, Tue May 22 21:55:31 2012 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 UTC

# Line 100 | Line 100 | namespace OpenMD {
100      //save statistics, before writeStat,  we must save statistics
101      thermo.saveStat();
102      saveConservedQuantity();
103 <    if (simParams->getUseRNEMD())
103 >    if (simParams->getRNEMDParameters()->getUseRNEMD())
104        rnemd_->getStarted();
105  
106      statWriter->writeStat(currentSnapshot_->statData);
# Line 111 | Line 111 | namespace OpenMD {
111      if (needReset) {
112        currReset = resetTime + currentSnapshot_->getTime();
113      }
114 <    if (simParams->getUseRNEMD()){
114 >    if (simParams->getRNEMDParameters()->getUseRNEMD()){
115        currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
116      }
117      needPotential = false;
# Line 174 | Line 174 | namespace OpenMD {
174        thermo.saveStat();
175        saveConservedQuantity();
176  
177 <      if (simParams->getUseRNEMD()) {
177 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
178          rnemd_->getStatus();
179        }
180  
# Line 215 | Line 215 | namespace OpenMD {
215  
216    void VelocityVerletIntegrator::calcForce() {
217      forceMan_->calcForces();
218 +    flucQ_->applyConstraints();
219    }
220  
221    DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
# Line 231 | Line 232 | namespace OpenMD {
232  
233  
234      if (simParams->getUseThermodynamicIntegration())
235 <      mask.set(Stats::VRAW);
235 >      mask.set(Stats::RAW_POTENTIAL);
236  
237      // if we've got restraints turned on, we'll also want a report of the
238      // total harmonic restraints
239      if (simParams->getUseRestraints()){
240 <      mask.set(Stats::VHARM);
240 >      mask.set(Stats::RESTRAINT_POTENTIAL);
241      }
242  
243      if (simParams->havePrintPressureTensor() &&
# Line 257 | Line 258 | namespace OpenMD {
258        mask.set(Stats::BOX_DIPOLE_Y);
259        mask.set(Stats::BOX_DIPOLE_Z);
260      }
261 +
262 +    if (simParams->getPrintHeatFlux()) {
263 +      mask.set(Stats::HEATFLUX_X);
264 +      mask.set(Stats::HEATFLUX_Y);
265 +      mask.set(Stats::HEATFLUX_Z);
266 +    }
267    
268      if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
269        if (simParams->getPrintTaggedPairDistance()) {
# Line 264 | Line 271 | namespace OpenMD {
271        }
272      }
273  
274 <    if (simParams->getUseRNEMD()) {
274 >    if (simParams->getRNEMDParameters()->getUseRNEMD()) {
275        mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
276      }
277      

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