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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 541 by tim, Sun May 22 21:05:15 2005 UTC vs.
Revision 1360 by cli2, Mon Sep 7 16:31:51 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 <    
93 <    if (simParams->getUseSolidThermInt()) {
94 <      restWriter = createRestWriter();
95 <      restWriter->writeZangle();
96 <    }
97 <    
94 >
95      dumpWriter->writeDumpAndEor();
96 <    
100 <    
96 >
97      //save statistics, before writeStat,  we must save statistics
98      thermo.saveStat();
99      saveConservedQuantity();
100 +    if (simParams->getUseRNEMD())
101 +      rnemd_->getStatus();
102 +
103      statWriter->writeStat(currentSnapshot_->statData);
104      
105      currSample = sampleTime + currentSnapshot_->getTime();
106 <    currStatus =  statusTime + currentSnapshot_->getTime();;
107 <    currThermal = thermalTime +  + currentSnapshot_->getTime();
106 >    currStatus =  statusTime + currentSnapshot_->getTime();
107 >    currThermal = thermalTime + currentSnapshot_->getTime();
108 >    if (needReset) {
109 >      currReset = resetTime + currentSnapshot_->getTime();
110 >    }
111 >    if (simParams->getUseRNEMD()){
112 >      currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
113 >    }
114      needPotential = false;
115      needStress = false;      
116      
# Line 132 | Line 137 | namespace oopse {
137  
138  
139    void VelocityVerletIntegrator::preStep() {
140 <    double difference = currentSnapshot_->getTime() + dt - currStatus;
140 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141    
142      if (difference > 0 || fabs(difference) < oopse::epsilon) {
143        needPotential = true;
144        needStress = true;  
145      }
141 –  
146    }
147  
148    void VelocityVerletIntegrator::postStep() {
149 <  
149 >
150      //save snapshot
151      info_->getSnapshotManager()->advance();
152    
153      //increase time
154      currentSnapshot_->increaseTime(dt);        
155 <  
155 >  
156      if (needVelocityScaling) {
157        if (currentSnapshot_->getTime() >= currThermal) {
158          velocitizer_->velocitize(targetScalingTemp);
159          currThermal += thermalTime;
160        }
161      }
162 <  
162 >    if (useRNEMD) {
163 >      if (currentSnapshot_->getTime() >= currRNEMD) {
164 >        rnemd_->doSwap();
165 >        currRNEMD += RNEMD_swapTime;
166 >      }
167 >    }
168 >    
169      if (currentSnapshot_->getTime() >= currSample) {
170        dumpWriter->writeDumpAndEor();
171 <    
162 <      if (simParams->getUseSolidThermInt())
163 <        restWriter->writeZangle();
164 <    
171 >      
172        currSample += sampleTime;
173      }
174 <  
174 >    
175      if (currentSnapshot_->getTime() >= currStatus) {
176        //save statistics, before writeStat,  we must save statistics
177        thermo.saveStat();
178        saveConservedQuantity();
179 +
180 +      if (simParams->getUseRNEMD())
181 +        rnemd_->getStatus();
182 +
183        statWriter->writeStat(currentSnapshot_->statData);
184 <    
184 >      
185        needPotential = false;
186        needStress = false;
187        currStatus += statusTime;
188      }
189 <  
190 <  
189 >    
190 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
191 >      resetIntegrator();
192 >      currReset += resetTime;
193 >    }        
194    }
195  
196  
197    void VelocityVerletIntegrator::finalize() {
198      dumpWriter->writeEor();
185 –  
186 –    if (simParams->getUseSolidThermInt()) {
187 –      restWriter->writeZangle();
188 –      delete restWriter;
189 –      restWriter = NULL;
190 –    }
199    
200      delete dumpWriter;
201      delete statWriter;
# Line 215 | Line 223 | namespace oopse {
223    }
224  
225    StatWriter* VelocityVerletIntegrator::createStatWriter() {
226 <    // if solidThermInt is true, add extra information to the statfile
227 <    if (simParams->getUseSolidThermInt()){
228 <      StatsBitSet mask;
229 <      mask.set(Stats::TIME);
230 <      mask.set(Stats::TOTAL_ENERGY);
231 <      mask.set(Stats::POTENTIAL_ENERGY);
232 <      mask.set(Stats::KINETIC_ENERGY);
233 <      mask.set(Stats::TEMPERATURE);
234 <      mask.set(Stats::PRESSURE);
227 <      mask.set(Stats::VOLUME);
228 <      mask.set(Stats::CONSERVED_QUANTITY);
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);
231 –      return new StatWriter(info_->getStatFileName(), mask);
241      }
242  
243 <    if (simParams->havePrintPresureTensor() && simParams->getPrintPressureTensor()){
244 <        mask.set(Stats::TIME);
245 <        mask.set(Stats::TOTAL_ENERGY);
246 <        mask.set(Stats::POTENTIAL_ENERGY);
247 <        mask.set(Stats::KINETIC_ENERGY);
248 <        mask.set(Stats::TEMPERATURE);
249 <        mask.set(Stats::PRESSURE);
250 <        mask.set(Stats::VOLUME);
251 <        mask.set(Stats::CONSERVED_QUANTITY);
252 <        mask.set(Stats::PRESSURE_TENSOR_X);
253 <        mask.set(Stats::PRESSURE_TENSOR_Y);
245 <        mask.set(Stats::PRESSURE_TENSOR_Z);
246 <        return new StatWriter(info_->getStatFileName(), mask);
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 <    return new StatWriter(info_->getStatFileName());
257 <  }
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 <  RestWriter* VelocityVerletIntegrator::createRestWriter(){
269 <    return new RestWriter(info_);
268 >    if (simParams->getUseRNEMD()) {
269 >      mask.set(Stats::RNEMD_SWAP_TOTAL);
270 >    }
271 >      
272 >
273 >     return new StatWriter(info_->getStatFileName(), mask);
274    }
275  
276  

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