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Comparing branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC vs.
Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

# 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 98 | Line 97 | namespace OpenMD {
97      progressBar = new ProgressBar();
98  
99      //save statistics, before writeStat,  we must save statistics
101 –    thermo.saveStat();
100      saveConservedQuantity();
101 <    if (simParams->getUseRNEMD())
101 >    stats->collectStats();
102 >
103 >    if (simParams->getRNEMDParameters()->getUseRNEMD())
104        rnemd_->getStarted();
105  
106 <    statWriter->writeStat(currentSnapshot_->statData);
106 >    statWriter->writeStat();
107      
108 <    currSample = sampleTime + currentSnapshot_->getTime();
109 <    currStatus =  statusTime + currentSnapshot_->getTime();
110 <    currThermal = thermalTime + currentSnapshot_->getTime();
108 >    currSample = sampleTime + snap->getTime();
109 >    currStatus =  statusTime + snap->getTime();
110 >    currThermal = thermalTime + snap->getTime();
111      if (needReset) {
112 <      currReset = resetTime + currentSnapshot_->getTime();
112 >      currReset = resetTime + snap->getTime();
113      }
114 <    if (simParams->getUseRNEMD()){
115 <      currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
114 >    if (simParams->getRNEMDParameters()->getUseRNEMD()){
115 >      currRNEMD = RNEMD_exchangeTime + snap->getTime();
116      }
117      needPotential = false;
118      needStress = false;      
# Line 123 | Line 123 | namespace OpenMD {
123    
124      initialize();
125    
126 <    while (currentSnapshot_->getTime() < runTime) {    
126 >    while (snap->getTime() < runTime) {    
127        preStep();    
128        integrateStep();    
129        postStep();      
# Line 133 | Line 133 | namespace OpenMD {
133  
134  
135    void VelocityVerletIntegrator::preStep() {
136 <    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
136 >    RealType difference = snap->getTime() + dt - currStatus;
137    
138      if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
139        needPotential = true;
# Line 147 | Line 147 | namespace OpenMD {
147      info_->getSnapshotManager()->advance();
148    
149      //increase time
150 <    currentSnapshot_->increaseTime(dt);        
150 >    snap->increaseTime(dt);        
151    
152      if (needVelocityScaling) {
153 <      if (currentSnapshot_->getTime() >= currThermal) {
153 >      if (snap->getTime() >= currThermal) {
154          velocitizer_->velocitize(targetScalingTemp);
155          currThermal += thermalTime;
156        }
157      }
158      if (useRNEMD) {
159 <      if (currentSnapshot_->getTime() >= currRNEMD) {
159 >      if (snap->getTime() >= currRNEMD) {
160          rnemd_->doRNEMD();
161          currRNEMD += RNEMD_exchangeTime;
162        }
163        rnemd_->collectData();
164      }
165      
166 <    if (currentSnapshot_->getTime() >= currSample) {
166 >    if (snap->getTime() >= currSample) {
167        dumpWriter->writeDumpAndEor();
168        
169        currSample += sampleTime;
170      }
171      
172 <    if (currentSnapshot_->getTime() >= currStatus) {
172 >    if (snap->getTime() >= currStatus) {
173        //save statistics, before writeStat,  we must save statistics
174 <      thermo.saveStat();
174 >      stats->collectStats();
175        saveConservedQuantity();
176  
177 <      if (simParams->getUseRNEMD()) {
178 <        rnemd_->getStatus();
177 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
178 >        rnemd_->writeOutputFile();
179        }
180  
181 <      statWriter->writeStat(currentSnapshot_->statData);
181 >      statWriter->writeStat();
182  
183 <      progressBar->setStatus(currentSnapshot_->getTime(), runTime);
183 >      progressBar->setStatus(snap->getTime(), runTime);
184        progressBar->update();
185  
186        needPotential = false;
# Line 188 | Line 188 | namespace OpenMD {
188        currStatus += statusTime;
189      }
190      
191 <    if (needReset && currentSnapshot_->getTime() >= currReset) {    
191 >    if (needReset && snap->getTime() >= currReset) {    
192        resetIntegrator();
193        currReset += resetTime;
194      }        
# Line 197 | Line 197 | namespace OpenMD {
197  
198    void VelocityVerletIntegrator::finalize() {
199      dumpWriter->writeEor();
200 <  
200 >    if (simParams->getRNEMDParameters()->getUseRNEMD()) {
201 >      rnemd_->writeOutputFile();
202 >    }
203 >
204      delete dumpWriter;
205      delete statWriter;
206    
# Line 223 | Line 226 | namespace OpenMD {
226    }
227  
228    StatWriter* VelocityVerletIntegrator::createStatWriter() {
226 –
227 –    std::string statFileFormatString = simParams->getStatFileFormat();
228 –    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
229 –  
230 –    // if we're doing a thermodynamic integration, we'll want the raw
231 –    // potential as well as the full potential:
232 –
233 –
234 –    if (simParams->getUseThermodynamicIntegration())
235 –      mask.set(Stats::VRAW);
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);
241 –    }
242 –
243 –    if (simParams->havePrintPressureTensor() &&
244 –        simParams->getPrintPressureTensor()){
245 –      mask.set(Stats::PRESSURE_TENSOR_XX);
246 –      mask.set(Stats::PRESSURE_TENSOR_XY);
247 –      mask.set(Stats::PRESSURE_TENSOR_XZ);
248 –      mask.set(Stats::PRESSURE_TENSOR_YX);
249 –      mask.set(Stats::PRESSURE_TENSOR_YY);
250 –      mask.set(Stats::PRESSURE_TENSOR_YZ);
251 –      mask.set(Stats::PRESSURE_TENSOR_ZX);
252 –      mask.set(Stats::PRESSURE_TENSOR_ZY);
253 –      mask.set(Stats::PRESSURE_TENSOR_ZZ);
254 –    }
229      
230 <    if (simParams->getAccumulateBoxDipole()) {
231 <      mask.set(Stats::BOX_DIPOLE_X);
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()) {
270 <        mask.set(Stats::TAGGED_PAIR_DISTANCE);
271 <      }
272 <    }
273 <
274 <    if (simParams->getUseRNEMD()) {
275 <      mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
276 <    }
230 >    stats = new Stats(info_);
231 >    statWriter = new StatWriter(info_->getStatFileName(), stats);
232      
233 <
279 <    return new StatWriter(info_->getStatFileName(), mask);
233 >    return statWriter;
234    }
235  
282 –
236   } //end namespace OpenMD

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