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Comparing branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC vs.
Revision 1760 by gezelter, Thu Jun 21 19:26:46 2012 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 53 | Line 54 | namespace OpenMD {
54   #include "utils/ProgressBar.hpp"
55  
56   namespace OpenMD {
57 <  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
57 >  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
58      dt2 = 0.5 * dt;
58 –    rotAlgo = new DLM();
59 –    rattle = new Rattle(info);
59    }
60    
61    VelocityVerletIntegrator::~VelocityVerletIntegrator() {
63 –    delete rotAlgo;
64 –    delete rattle;
62    }
63    
64    void VelocityVerletIntegrator::initialize(){
65      
66 <    forceMan_->init();
66 >    forceMan_->initialize();
67      
68      // remove center of mass drift velocity (in case we passed in a
69      // configuration that was drifting)
70      velocitizer_->removeComDrift();
71 +
72 +    // find the initial fluctuating charges.
73 +    flucQ_->initialize();
74      
75      // initialize the forces before the first step
76      calcForce();
# Line 78 | Line 78 | namespace OpenMD {
78      // execute the constraint algorithm to make sure that the system is
79      // constrained at the very beginning  
80      if (info_->getNGlobalConstraints() > 0) {
81 <      rattle->constraintA();
81 >      rattle_->constraintA();
82        calcForce();
83 <      rattle->constraintB();      
83 >      rattle_->constraintB();      
84        //copy the current snapshot to previous snapshot
85        info_->getSnapshotManager()->advance();
86      }
# 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 121 | Line 121 | namespace OpenMD {
121  
122    void VelocityVerletIntegrator::doIntegrate() {
123    
124 –  
124      initialize();
125    
126 <    while (currentSnapshot_->getTime() < runTime) {
127 <    
128 <      preStep();
129 <    
130 <      integrateStep();
132 <    
133 <      postStep();
134 <      
135 <    }
136 <  
126 >    while (currentSnapshot_->getTime() < runTime) {    
127 >      preStep();    
128 >      integrateStep();    
129 >      postStep();      
130 >    }  
131      finalize();
138 –  
132    }
133  
134  
# Line 181 | 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 210 | Line 203 | namespace OpenMD {
203    
204      dumpWriter = NULL;
205      statWriter = NULL;
213 –  
206    }
207  
208    void VelocityVerletIntegrator::integrateStep() {
# Line 223 | Line 215 | namespace OpenMD {
215  
216    void VelocityVerletIntegrator::calcForce() {
217      forceMan_->calcForces();
218 +    flucQ_->applyConstraints();
219    }
220  
221    DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
# Line 239 | 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 265 | 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 272 | 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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