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root/OpenMD/trunk/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 1341 by skuang, Fri May 8 19:47:05 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 +    if (simParams->getUseRNEMD())
106 +      rnemd_->getStatus();
107 +
108      statWriter->writeStat(currentSnapshot_->statData);
109      
110      currSample = sampleTime + currentSnapshot_->getTime();
111 <    currStatus =  statusTime + currentSnapshot_->getTime();;
111 >    currStatus =  statusTime + currentSnapshot_->getTime();
112      currThermal = thermalTime + currentSnapshot_->getTime();
113      if (needReset) {
114        currReset = resetTime + currentSnapshot_->getTime();
115      }
116 +    if (simParams->getUseRNEMD()){
117 +      currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
118 +    }
119      needPotential = false;
120      needStress = false;      
121      
# Line 135 | Line 142 | namespace oopse {
142  
143  
144    void VelocityVerletIntegrator::preStep() {
145 <    double difference = currentSnapshot_->getTime() + dt - currStatus;
145 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
146    
147      if (difference > 0 || fabs(difference) < oopse::epsilon) {
148        needPotential = true;
149        needStress = true;  
150      }
144 –
151    }
152  
153    void VelocityVerletIntegrator::postStep() {
# Line 151 | Line 157 | namespace oopse {
157    
158      //increase time
159      currentSnapshot_->increaseTime(dt);        
160 <  
160 >  
161      if (needVelocityScaling) {
162        if (currentSnapshot_->getTime() >= currThermal) {
163          velocitizer_->velocitize(targetScalingTemp);
164          currThermal += thermalTime;
165        }
166      }
167 <  
167 >    if (useRNEMD) {
168 >      if (currentSnapshot_->getTime() >= currRNEMD) {
169 >        rnemd_->doSwap();
170 >        currRNEMD += RNEMD_swapTime;
171 >      }
172 >    }
173 >    
174      if (currentSnapshot_->getTime() >= currSample) {
175        dumpWriter->writeDumpAndEor();
176 <    
176 >      
177        if (simParams->getUseSolidThermInt())
178 <        restWriter->writeZangle();
179 <    
178 >        restWriter->writeZAngFile();
179 >      
180        currSample += sampleTime;
181      }
182 <  
182 >    
183      if (currentSnapshot_->getTime() >= currStatus) {
184        //save statistics, before writeStat,  we must save statistics
185        thermo.saveStat();
186        saveConservedQuantity();
187 +
188 +      if (simParams->getUseRNEMD())
189 +        rnemd_->getStatus();
190 +
191        statWriter->writeStat(currentSnapshot_->statData);
192 <    
192 >      
193        needPotential = false;
194        needStress = false;
195        currStatus += statusTime;
196      }
197 <
198 <      if (needReset && currentSnapshot_->getTime() >= currReset) {    
199 <        resetIntegrator();
200 <        currReset += resetTime;
201 <      }
186 <  
197 >    
198 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
199 >      resetIntegrator();
200 >      currReset += resetTime;
201 >    }        
202    }
203  
204  
# Line 191 | Line 206 | namespace oopse {
206      dumpWriter->writeEor();
207    
208      if (simParams->getUseSolidThermInt()) {
209 <      restWriter->writeZangle();
209 >      restWriter->writeZAngFile();
210        delete restWriter;
211        restWriter = NULL;
212      }
# Line 232 | Line 247 | namespace oopse {
247        mask.set(Stats::VHARM);
248      }
249  
250 <    if (simParams->havePrintPressureTensor() && simParams->getPrintPressureTensor()){
251 <        mask.set(Stats::PRESSURE_TENSOR_X);
252 <        mask.set(Stats::PRESSURE_TENSOR_Y);
253 <        mask.set(Stats::PRESSURE_TENSOR_Z);
250 >    if (simParams->havePrintPressureTensor() &&
251 >        simParams->getPrintPressureTensor()){
252 >      mask.set(Stats::PRESSURE_TENSOR_XX);
253 >      mask.set(Stats::PRESSURE_TENSOR_XY);
254 >      mask.set(Stats::PRESSURE_TENSOR_XZ);
255 >      mask.set(Stats::PRESSURE_TENSOR_YX);
256 >      mask.set(Stats::PRESSURE_TENSOR_YY);
257 >      mask.set(Stats::PRESSURE_TENSOR_YZ);
258 >      mask.set(Stats::PRESSURE_TENSOR_ZX);
259 >      mask.set(Stats::PRESSURE_TENSOR_ZY);
260 >      mask.set(Stats::PRESSURE_TENSOR_ZZ);
261      }
262      
263 +    if (simParams->getAccumulateBoxDipole()) {
264 +      mask.set(Stats::BOX_DIPOLE_X);
265 +      mask.set(Stats::BOX_DIPOLE_Y);
266 +      mask.set(Stats::BOX_DIPOLE_Z);
267 +    }
268 +  
269 +    if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
270 +      if (simParams->getPrintTaggedPairDistance()) {
271 +        mask.set(Stats::TAGGED_PAIR_DISTANCE);
272 +      }
273 +    }
274 +
275 +    if (simParams->getUseRNEMD()) {
276 +      mask.set(Stats::RNEMD_SWAP_TOTAL);
277 +    }
278 +      
279 +
280       return new StatWriter(info_->getStatFileName(), mask);
281    }
282  

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