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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 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 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 143 | Line 143 | namespace OpenMD {
143  
144    void VelocityVerletIntegrator::postStep() {
145  
146 –    //save snapshot
147 –    info_->getSnapshotManager()->advance();
148 –  
149 –    //increase time
150 –    currentSnapshot_->increaseTime(dt);        
146    
147      if (needVelocityScaling) {
148 <      if (currentSnapshot_->getTime() >= currThermal) {
148 >      if (snap->getTime() >= currThermal) {
149          velocitizer_->velocitize(targetScalingTemp);
150          currThermal += thermalTime;
151        }
152      }
153      if (useRNEMD) {
154 <      if (currentSnapshot_->getTime() >= currRNEMD) {
154 >      if (snap->getTime() >= currRNEMD) {
155          rnemd_->doRNEMD();
156          currRNEMD += RNEMD_exchangeTime;
157        }
158        rnemd_->collectData();
159      }
160      
161 <    if (currentSnapshot_->getTime() >= currSample) {
161 >    if (snap->getTime() >= currSample) {
162        dumpWriter->writeDumpAndEor();
163        
164        currSample += sampleTime;
165      }
166      
167 <    if (currentSnapshot_->getTime() >= currStatus) {
167 >    if (snap->getTime() >= currStatus) {
168        //save statistics, before writeStat,  we must save statistics
174 –      thermo.saveStat();
169        saveConservedQuantity();
170 +      stats->collectStats();
171  
172 <      if (simParams->getUseRNEMD()) {
173 <        rnemd_->getStatus();
172 >      if (simParams->getRNEMDParameters()->getUseRNEMD()) {
173 >        rnemd_->writeOutputFile();
174        }
175  
176 <      statWriter->writeStat(currentSnapshot_->statData);
176 >      statWriter->writeStat();
177  
178 <      progressBar->setStatus(currentSnapshot_->getTime(), runTime);
178 >      progressBar->setStatus(snap->getTime(), runTime);
179        progressBar->update();
180  
181        needPotential = false;
# Line 188 | Line 183 | namespace OpenMD {
183        currStatus += statusTime;
184      }
185      
186 <    if (needReset && currentSnapshot_->getTime() >= currReset) {    
186 >    if (needReset && snap->getTime() >= currReset) {    
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 <  
201 >    if (simParams->getRNEMDParameters()->getUseRNEMD()) {
202 >      rnemd_->writeOutputFile();
203 >    }
204 >
205      delete dumpWriter;
206      delete statWriter;
207    
# Line 215 | Line 219 | namespace OpenMD {
219  
220    void VelocityVerletIntegrator::calcForce() {
221      forceMan_->calcForces();
222 +    flucQ_->applyConstraints();
223    }
224  
225    DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
# Line 222 | Line 227 | namespace OpenMD {
227    }
228  
229    StatWriter* VelocityVerletIntegrator::createStatWriter() {
225 –
226 –    std::string statFileFormatString = simParams->getStatFileFormat();
227 –    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
228 –  
229 –    // if we're doing a thermodynamic integration, we'll want the raw
230 –    // potential as well as the full potential:
231 –
232 –
233 –    if (simParams->getUseThermodynamicIntegration())
234 –      mask.set(Stats::VRAW);
235 –
236 –    // if we've got restraints turned on, we'll also want a report of the
237 –    // total harmonic restraints
238 –    if (simParams->getUseRestraints()){
239 –      mask.set(Stats::VHARM);
240 –    }
241 –
242 –    if (simParams->havePrintPressureTensor() &&
243 –        simParams->getPrintPressureTensor()){
244 –      mask.set(Stats::PRESSURE_TENSOR_XX);
245 –      mask.set(Stats::PRESSURE_TENSOR_XY);
246 –      mask.set(Stats::PRESSURE_TENSOR_XZ);
247 –      mask.set(Stats::PRESSURE_TENSOR_YX);
248 –      mask.set(Stats::PRESSURE_TENSOR_YY);
249 –      mask.set(Stats::PRESSURE_TENSOR_YZ);
250 –      mask.set(Stats::PRESSURE_TENSOR_ZX);
251 –      mask.set(Stats::PRESSURE_TENSOR_ZY);
252 –      mask.set(Stats::PRESSURE_TENSOR_ZZ);
253 –    }
230      
231 <    if (simParams->getAccumulateBoxDipole()) {
232 <      mask.set(Stats::BOX_DIPOLE_X);
257 <      mask.set(Stats::BOX_DIPOLE_Y);
258 <      mask.set(Stats::BOX_DIPOLE_Z);
259 <    }
260 <  
261 <    if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
262 <      if (simParams->getPrintTaggedPairDistance()) {
263 <        mask.set(Stats::TAGGED_PAIR_DISTANCE);
264 <      }
265 <    }
266 <
267 <    if (simParams->getUseRNEMD()) {
268 <      mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
269 <    }
231 >    stats = new Stats(info_);
232 >    statWriter = new StatWriter(info_->getStatFileName(), stats);
233      
234 <
272 <    return new StatWriter(info_->getStatFileName(), mask);
234 >    return statWriter;
235    }
236  
275 –
237   } //end namespace OpenMD

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