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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 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 1329 by gezelter, Sat Mar 14 01:23:53 2009 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# 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();;
109 <    currThermal = thermalTime +  + 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      
119 < }
119 >  }
120  
121 < void VelocityVerletIntegrator::doIntegrate() {
121 >  void VelocityVerletIntegrator::doIntegrate() {
122    
123    
124 <  initialize();
124 >    initialize();
125    
126 <  while (currentSnapshot_->getTime() < runTime) {
126 >    while (currentSnapshot_->getTime() < runTime) {
127      
128 <    preStep();
128 >      preStep();
129      
130 <    integrateStep();
130 >      integrateStep();
131      
132 <    postStep();
132 >      postStep();
133      
134 <  }
134 >    }
135    
136 <  finalize();
136 >    finalize();
137    
138 < }
138 >  }
139  
140  
141 < void VelocityVerletIntegrator::preStep() {
142 <  double difference = currentSnapshot_->getTime() + dt - currStatus;
141 >  void VelocityVerletIntegrator::preStep() {
142 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
143    
144 <  if (difference > 0 || fabs(difference) < oopse::epsilon) {
145 <    needPotential = true;
146 <    needStress = true;  
144 >    if (difference > 0 || fabs(difference) < oopse::epsilon) {
145 >      needPotential = true;
146 >      needStress = true;  
147 >    }
148    }
141 –  
142 – }
149  
150 < void VelocityVerletIntegrator::postStep() {
150 >  void VelocityVerletIntegrator::postStep() {
151 >
152 >    //save snapshot
153 >    info_->getSnapshotManager()->advance();
154    
155 <  //save snapshot
156 <  info_->getSnapshotManager()->advance();
157 <  
158 <  //increase time
159 <  currentSnapshot_->increaseTime(dt);        
160 <  
161 <  if (needVelocityScaling) {
162 <    if (currentSnapshot_->getTime() >= currThermal) {
154 <      velocitizer_->velocitize(targetScalingTemp);
155 <      currThermal += thermalTime;
155 >    //increase time
156 >    currentSnapshot_->increaseTime(dt);        
157 >  
158 >    if (needVelocityScaling) {
159 >      if (currentSnapshot_->getTime() >= currThermal) {
160 >        velocitizer_->velocitize(targetScalingTemp);
161 >        currThermal += thermalTime;
162 >      }
163      }
164 <  }
165 <  
166 <  if (currentSnapshot_->getTime() >= currSample) {
167 <    dumpWriter->writeDumpAndEor();
164 >    if (useRNEMD) {
165 >      if (currentSnapshot_->getTime() >= currRNEMD) {
166 >        rnemd_->doSwap();
167 >        currRNEMD += RNEMD_swapTime;
168 >      }
169 >    }
170      
171 <    if (simParams->getUseSolidThermInt())
172 <      restWriter->writeZangle();
171 >    if (currentSnapshot_->getTime() >= currSample) {
172 >      dumpWriter->writeDumpAndEor();
173 >      
174 >      if (simParams->getUseSolidThermInt())
175 >        restWriter->writeZAngFile();
176 >      
177 >      currSample += sampleTime;
178 >    }
179      
180 <    currSample += sampleTime;
181 <  }
182 <  
183 <  if (currentSnapshot_->getTime() >= currStatus) {
184 <    //save statistics, before writeStat,  we must save statistics
185 <    thermo.saveStat();
186 <    saveConservedQuantity();
187 <    statWriter->writeStat(currentSnapshot_->statData);
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 >      
186 >      needPotential = false;
187 >      needStress = false;
188 >      currStatus += statusTime;
189 >    }
190      
191 <    needPotential = false;
192 <    needStress = false;
193 <    currStatus += statusTime;
191 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
192 >      resetIntegrator();
193 >      currReset += resetTime;
194 >    }        
195    }
196 +
197 +
198 +  void VelocityVerletIntegrator::finalize() {
199 +    dumpWriter->writeEor();
200    
201 +    if (simParams->getUseSolidThermInt()) {
202 +      restWriter->writeZAngFile();
203 +      delete restWriter;
204 +      restWriter = NULL;
205 +    }
206    
207 < }
208 <
182 <
183 < void VelocityVerletIntegrator::finalize() {
184 <  dumpWriter->writeEor();
207 >    delete dumpWriter;
208 >    delete statWriter;
209    
210 <  if (simParams->getUseSolidThermInt()) {
211 <    restWriter->writeZangle();
188 <    delete restWriter;
189 <    restWriter = NULL;
190 <  }
210 >    dumpWriter = NULL;
211 >    statWriter = NULL;
212    
213 <  delete dumpWriter;
193 <  delete statWriter;
194 <  
195 <  dumpWriter = NULL;
196 <  statWriter = NULL;
197 <  
198 < }
213 >  }
214  
215 < void VelocityVerletIntegrator::integrateStep() {
215 >  void VelocityVerletIntegrator::integrateStep() {
216    
217 <  moveA();
218 <  calcForce(needPotential, needStress);
219 <  moveB();
220 < }
217 >    moveA();
218 >    calcForce(needPotential, needStress);
219 >    moveB();
220 >  }
221  
222  
223 < void VelocityVerletIntegrator::calcForce(bool needPotential,
224 <                                         bool needStress) {
225 <  forceMan_->calcForces(needPotential, needStress);
226 < }
223 >  void VelocityVerletIntegrator::calcForce(bool needPotential,
224 >                                           bool needStress) {
225 >    forceMan_->calcForces(needPotential, needStress);
226 >  }
227  
228 < DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
229 <  return new DumpWriter(info_);
230 < }
228 >  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
229 >    return new DumpWriter(info_);
230 >  }
231  
232 < StatWriter* VelocityVerletIntegrator::createStatWriter() {
233 <  // if solidThermInt is true, add extra information to the statfile
234 <  if (simParams->getUseSolidThermInt()){
235 <    StatsBitSet mask;
236 <    mask.set(Stats::TIME);
237 <    mask.set(Stats::TOTAL_ENERGY);
238 <    mask.set(Stats::POTENTIAL_ENERGY);
239 <    mask.set(Stats::KINETIC_ENERGY);
240 <    mask.set(Stats::TEMPERATURE);
241 <    mask.set(Stats::PRESSURE);
242 <    mask.set(Stats::CONSERVED_QUANTITY);
243 <    mask.set(Stats::VRAW);
244 <    mask.set(Stats::VHARM);
245 <    return new StatWriter(info_->getStatFileName(), mask);
232 >  StatWriter* VelocityVerletIntegrator::createStatWriter() {
233 >
234 >    std::string statFileFormatString = simParams->getStatFileFormat();
235 >    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
236 >    
237 >    // if solidThermInt is true, add extra information to the statfile
238 >    if (simParams->getUseSolidThermInt()){
239 >      mask.set(Stats::VRAW);
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 >    }
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    }
232 –  
233 –  return new StatWriter(info_->getStatFileName());
234 – }
275  
276 < RestWriter* VelocityVerletIntegrator::createRestWriter(){
277 <  return new RestWriter(info_);
278 < }
276 >  RestWriter* VelocityVerletIntegrator::createRestWriter(){
277 >    return new RestWriter(info_);
278 >  }
279  
280  
281   } //end namespace oopse

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