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root/OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.cpp
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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1329 by gezelter, Sat Mar 14 01:23:53 2009 UTC

# Line 67 | Line 67 | namespace oopse {
67      
68      forceMan_->init();
69      
70 <    // remove center of mass drift velocity (in case we passed in a configuration
71 <    // that was drifting
70 >    // remove center of mass drift velocity (in case we passed in a
71 >    // configuration that was drifting)
72      velocitizer_->removeComDrift();
73      
74      // initialize the forces before the first step
75      calcForce(true, true);
76      
77 <    //execute constraint algorithm to make sure at the very beginning the system is constrained  
77 >    // execute the constraint algorithm to make sure that the system is
78 >    // constrained at the very beginning  
79      if (info_->getNGlobalConstraints() > 0) {
80        rattle->constraintA();
81        calcForce(true, true);
82 <      rattle->constraintB();        
83 <      info_->getSnapshotManager()->advance();//copy the current snapshot to previous snapshot
82 >      rattle->constraintB();      
83 >      //copy the current snapshot to previous snapshot
84 >      info_->getSnapshotManager()->advance();
85      }
86      
87      if (needVelocityScaling) {
# Line 89 | Line 91 | namespace oopse {
91      dumpWriter = createDumpWriter();
92      
93      statWriter = createStatWriter();
94 <    
94 >
95 >    dumpWriter->writeDumpAndEor();
96 >
97      if (simParams->getUseSolidThermInt()) {
98        restWriter = createRestWriter();
99 <      restWriter->writeZangle();
99 >      restWriter->writeZAngFile();
100      }
101      
98 –    dumpWriter->writeDumpAndEor();
99 –    
100 –    
102      //save statistics, before writeStat,  we must save statistics
103      thermo.saveStat();
104      saveConservedQuantity();
105      statWriter->writeStat(currentSnapshot_->statData);
106      
107      currSample = sampleTime + currentSnapshot_->getTime();
108 <    currStatus =  statusTime + currentSnapshot_->getTime();;
108 >    currStatus =  statusTime + currentSnapshot_->getTime();
109      currThermal = thermalTime + currentSnapshot_->getTime();
110      if (needReset) {
111        currReset = resetTime + currentSnapshot_->getTime();
112      }
113 +    if (simParams->getUseRNEMD()){
114 +      currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
115 +    }
116      needPotential = false;
117      needStress = false;      
118      
# Line 135 | Line 139 | namespace oopse {
139  
140  
141    void VelocityVerletIntegrator::preStep() {
142 <    double difference = currentSnapshot_->getTime() + dt - currStatus;
142 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
143    
144      if (difference > 0 || fabs(difference) < oopse::epsilon) {
145        needPotential = true;
146        needStress = true;  
147      }
144 –
148    }
149  
150    void VelocityVerletIntegrator::postStep() {
# Line 151 | Line 154 | namespace oopse {
154    
155      //increase time
156      currentSnapshot_->increaseTime(dt);        
157 <  
157 >  
158      if (needVelocityScaling) {
159        if (currentSnapshot_->getTime() >= currThermal) {
160          velocitizer_->velocitize(targetScalingTemp);
161          currThermal += thermalTime;
162        }
163      }
164 <  
164 >    if (useRNEMD) {
165 >      if (currentSnapshot_->getTime() >= currRNEMD) {
166 >        rnemd_->doSwap();
167 >        currRNEMD += RNEMD_swapTime;
168 >      }
169 >    }
170 >    
171      if (currentSnapshot_->getTime() >= currSample) {
172        dumpWriter->writeDumpAndEor();
173 <    
173 >      
174        if (simParams->getUseSolidThermInt())
175 <        restWriter->writeZangle();
176 <    
175 >        restWriter->writeZAngFile();
176 >      
177        currSample += sampleTime;
178      }
179 <  
179 >    
180      if (currentSnapshot_->getTime() >= currStatus) {
181        //save statistics, before writeStat,  we must save statistics
182        thermo.saveStat();
183        saveConservedQuantity();
184        statWriter->writeStat(currentSnapshot_->statData);
185 <    
185 >      
186        needPotential = false;
187        needStress = false;
188        currStatus += statusTime;
189      }
190 <
191 <      if (needReset && currentSnapshot_->getTime() >= currReset) {    
192 <        resetIntegrator();
193 <        currReset += resetTime;
194 <      }
186 <  
190 >    
191 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
192 >      resetIntegrator();
193 >      currReset += resetTime;
194 >    }        
195    }
196  
197  
# Line 191 | Line 199 | namespace oopse {
199      dumpWriter->writeEor();
200    
201      if (simParams->getUseSolidThermInt()) {
202 <      restWriter->writeZangle();
202 >      restWriter->writeZAngFile();
203        delete restWriter;
204        restWriter = NULL;
205      }
# Line 232 | Line 240 | namespace oopse {
240        mask.set(Stats::VHARM);
241      }
242  
243 <    if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
244 <        mask.set(Stats::PRESSURE_TENSOR_X);
245 <        mask.set(Stats::PRESSURE_TENSOR_Y);
246 <        mask.set(Stats::PRESSURE_TENSOR_Z);
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      }
255      
256 +    if (simParams->getAccumulateBoxDipole()) {
257 +      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->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
263 +      if (simParams->getPrintTaggedPairDistance()) {
264 +        mask.set(Stats::TAGGED_PAIR_DISTANCE);
265 +      }
266 +    }
267 +
268 +    if (simParams->getUseRNEMD()) {
269 +      mask.set(Stats::RNEMD_SWAP_TOTAL);
270 +    }
271 +      
272 +
273       return new StatWriter(info_->getStatFileName(), mask);
274    }
275  

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