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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 1360 by cli2, Mon Sep 7 16:31:51 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 <    
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      
117 < }
117 >  }
118  
119 < void VelocityVerletIntegrator::doIntegrate() {
119 >  void VelocityVerletIntegrator::doIntegrate() {
120    
121    
122 <  initialize();
122 >    initialize();
123    
124 <  while (currentSnapshot_->getTime() < runTime) {
124 >    while (currentSnapshot_->getTime() < runTime) {
125      
126 <    preStep();
126 >      preStep();
127      
128 <    integrateStep();
128 >      integrateStep();
129      
130 <    postStep();
130 >      postStep();
131      
132 <  }
132 >    }
133    
134 <  finalize();
134 >    finalize();
135    
136 < }
136 >  }
137  
138  
139 < void VelocityVerletIntegrator::preStep() {
140 <  double difference = currentSnapshot_->getTime() + dt - currStatus;
139 >  void VelocityVerletIntegrator::preStep() {
140 >    RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141    
142 <  if (difference > 0 || fabs(difference) < oopse::epsilon) {
143 <    needPotential = true;
144 <    needStress = true;  
142 >    if (difference > 0 || fabs(difference) < oopse::epsilon) {
143 >      needPotential = true;
144 >      needStress = true;  
145 >    }
146    }
141 –  
142 – }
147  
148 < void VelocityVerletIntegrator::postStep() {
148 >  void VelocityVerletIntegrator::postStep() {
149 >
150 >    //save snapshot
151 >    info_->getSnapshotManager()->advance();
152    
153 <  //save snapshot
154 <  info_->getSnapshotManager()->advance();
155 <  
156 <  //increase time
157 <  currentSnapshot_->increaseTime(dt);        
158 <  
159 <  if (needVelocityScaling) {
160 <    if (currentSnapshot_->getTime() >= currThermal) {
154 <      velocitizer_->velocitize(targetScalingTemp);
155 <      currThermal += thermalTime;
153 >    //increase time
154 >    currentSnapshot_->increaseTime(dt);        
155 >  
156 >    if (needVelocityScaling) {
157 >      if (currentSnapshot_->getTime() >= currThermal) {
158 >        velocitizer_->velocitize(targetScalingTemp);
159 >        currThermal += thermalTime;
160 >      }
161      }
162 <  }
163 <  
164 <  if (currentSnapshot_->getTime() >= currSample) {
165 <    dumpWriter->writeDumpAndEor();
162 >    if (useRNEMD) {
163 >      if (currentSnapshot_->getTime() >= currRNEMD) {
164 >        rnemd_->doSwap();
165 >        currRNEMD += RNEMD_swapTime;
166 >      }
167 >    }
168      
169 <    if (simParams->getUseSolidThermInt())
170 <      restWriter->writeZangle();
169 >    if (currentSnapshot_->getTime() >= currSample) {
170 >      dumpWriter->writeDumpAndEor();
171 >      
172 >      currSample += sampleTime;
173 >    }
174      
175 <    currSample += sampleTime;
176 <  }
177 <  
178 <  if (currentSnapshot_->getTime() >= currStatus) {
179 <    //save statistics, before writeStat,  we must save statistics
180 <    thermo.saveStat();
181 <    saveConservedQuantity();
182 <    statWriter->writeStat(currentSnapshot_->statData);
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 >      
185 >      needPotential = false;
186 >      needStress = false;
187 >      currStatus += statusTime;
188 >    }
189      
190 <    needPotential = false;
191 <    needStress = false;
192 <    currStatus += statusTime;
190 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
191 >      resetIntegrator();
192 >      currReset += resetTime;
193 >    }        
194    }
178 –  
179 –  
180 – }
195  
196  
197 < void VelocityVerletIntegrator::finalize() {
198 <  dumpWriter->writeEor();
197 >  void VelocityVerletIntegrator::finalize() {
198 >    dumpWriter->writeEor();
199    
200 <  if (simParams->getUseSolidThermInt()) {
201 <    restWriter->writeZangle();
188 <    delete restWriter;
189 <    restWriter = NULL;
190 <  }
200 >    delete dumpWriter;
201 >    delete statWriter;
202    
203 <  delete dumpWriter;
204 <  delete statWriter;
203 >    dumpWriter = NULL;
204 >    statWriter = NULL;
205    
206 <  dumpWriter = NULL;
196 <  statWriter = NULL;
197 <  
198 < }
206 >  }
207  
208 < void VelocityVerletIntegrator::integrateStep() {
208 >  void VelocityVerletIntegrator::integrateStep() {
209    
210 <  moveA();
211 <  calcForce(needPotential, needStress);
212 <  moveB();
213 < }
210 >    moveA();
211 >    calcForce(needPotential, needStress);
212 >    moveB();
213 >  }
214  
215  
216 < void VelocityVerletIntegrator::calcForce(bool needPotential,
217 <                                         bool needStress) {
218 <  forceMan_->calcForces(needPotential, needStress);
219 < }
216 >  void VelocityVerletIntegrator::calcForce(bool needPotential,
217 >                                           bool needStress) {
218 >    forceMan_->calcForces(needPotential, needStress);
219 >  }
220  
221 < DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
222 <  return new DumpWriter(info_);
215 < }
216 <
217 < StatWriter* VelocityVerletIntegrator::createStatWriter() {
218 <  // if solidThermInt is true, add extra information to the statfile
219 <  if (simParams->getUseSolidThermInt()){
220 <    StatsBitSet mask;
221 <    mask.set(Stats::TIME);
222 <    mask.set(Stats::TOTAL_ENERGY);
223 <    mask.set(Stats::POTENTIAL_ENERGY);
224 <    mask.set(Stats::KINETIC_ENERGY);
225 <    mask.set(Stats::TEMPERATURE);
226 <    mask.set(Stats::PRESSURE);
227 <    mask.set(Stats::CONSERVED_QUANTITY);
228 <    mask.set(Stats::VRAW);
229 <    mask.set(Stats::VHARM);
230 <    return new StatWriter(info_->getStatFileName(), mask);
221 >  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
222 >    return new DumpWriter(info_);
223    }
232 –  
233 –  return new StatWriter(info_->getStatFileName());
234 – }
224  
225 < RestWriter* VelocityVerletIntegrator::createRestWriter(){
237 <  return new RestWriter(info_);
238 < }
225 >  StatWriter* VelocityVerletIntegrator::createStatWriter() {
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);
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 +  }
275 +
276 +
277   } //end namespace oopse

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