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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 276 by tim, Wed Jan 26 15:26:47 2005 UTC vs.
Revision 1338 by skuang, Thu Apr 23 18:22:30 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 52 | Line 52 | namespace oopse {
52   #include "utils/StringUtils.hpp"
53  
54   namespace oopse {
55 < VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
55 >  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56      dt2 = 0.5 * dt;
57      rotAlgo = new DLM();
58      rattle = new Rattle(info);
59 < }
60 <
61 < VelocityVerletIntegrator::~VelocityVerletIntegrator() {
59 >  }
60 >  
61 >  VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62      delete rotAlgo;
63      delete rattle;
64 < }
65 <
66 < void VelocityVerletIntegrator::initialize(){
67 <
64 >  }
65 >  
66 >  void VelocityVerletIntegrator::initialize(){
67 >    
68      forceMan_->init();
69 <
70 <    // remove center of mass drift velocity (in case we passed in a configuration
71 <    // that was drifting
69 >    
70 >    // remove center of mass drift velocity (in case we passed in a
71 >    // configuration that was drifting)
72      velocitizer_->removeComDrift();
73 <
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  
76 >    
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
80 >      rattle->constraintA();
81 >      calcForce(true, true);
82 >      rattle->constraintB();      
83 >      //copy the current snapshot to previous snapshot
84 >      info_->getSnapshotManager()->advance();
85      }
86 <
86 >    
87      if (needVelocityScaling) {
88 <        velocitizer_->velocitize(targetScalingTemp);
88 >      velocitizer_->velocitize(targetScalingTemp);
89      }
90      
91      dumpWriter = createDumpWriter();
92 <    eorWriter = createEorWriter();
92 >    
93      statWriter = createStatWriter();
94 +
95 +    dumpWriter->writeDumpAndEor();
96  
97 <    dumpWriter->writeDump();
98 <    eorWriter->writeDump();
97 >    if (simParams->getUseSolidThermInt()) {
98 >      restWriter = createRestWriter();
99 >      restWriter->writeZAngFile();
100 >    }
101      
102      //save statistics, before writeStat,  we must save statistics
103      thermo.saveStat();
104      saveConservedQuantity();
105      statWriter->writeStat(currentSnapshot_->statData);
106 <
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 < }
108 <        
109 < void VelocityVerletIntegrator::doIntegrate() {
118 >    
119 >  }
120  
121 <
121 >  void VelocityVerletIntegrator::doIntegrate() {
122 >  
123 >  
124      initialize();
125 <
125 >  
126      while (currentSnapshot_->getTime() < runTime) {
127 <        
128 <        preStep();
129 <
130 <        integrateStep();
131 <        
132 <        postStep();
133 <
127 >    
128 >      preStep();
129 >    
130 >      integrateStep();
131 >    
132 >      postStep();
133 >    
134      }
135 <
135 >  
136      finalize();
137 <    
138 < }
137 >  
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;  
147 >    }
148 >  }
149  
150 <        if (difference > 0 || fabs(difference) < oopse::epsilon) {
133 <            needPotential = true;
134 <            needStress = true;  
135 <        }
150 >  void VelocityVerletIntegrator::postStep() {
151  
152 < }
152 >    //save snapshot
153 >    info_->getSnapshotManager()->advance();
154 >  
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 >    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 >      
174 >      if (simParams->getUseSolidThermInt())
175 >        restWriter->writeZAngFile();
176 >      
177 >      currSample += sampleTime;
178 >    }
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 >      if (simParams->getUseRNEMD())
186 >        rnemd_->getStatus();
187 >      
188 >      needPotential = false;
189 >      needStress = false;
190 >      currStatus += statusTime;
191 >    }
192 >    
193 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
194 >      resetIntegrator();
195 >      currReset += resetTime;
196 >    }        
197 >  }
198  
139 – void VelocityVerletIntegrator::postStep() {
199  
200 <        //save snapshot
201 <        info_->getSnapshotManager()->advance();
202 <
203 <        //increase time
204 <        currentSnapshot_->increaseTime(dt);        
205 <        
206 <        if (needVelocityScaling) {
207 <            if (currentSnapshot_->getTime() >= currThermal) {
208 <                velocitizer_->velocitize(targetScalingTemp);
150 <                currThermal += thermalTime;
151 <            }
152 <        }
153 <
154 <        if (currentSnapshot_->getTime() >= currSample) {
155 <            dumpWriter->writeDump();
156 <            eorWriter->writeDump();
157 <            currSample += sampleTime;
158 <        }
159 <
160 <        if (currentSnapshot_->getTime() >= currStatus) {
161 <            //save statistics, before writeStat,  we must save statistics
162 <            thermo.saveStat();
163 <            saveConservedQuantity();
164 <            statWriter->writeStat(currentSnapshot_->statData);
165 <
166 <            needPotential = false;
167 <            needStress = false;
168 <            currStatus += statusTime;
169 <        }
170 <
171 <        
172 < }
173 <
174 <
175 < void VelocityVerletIntegrator::finalize() {
176 <
177 <    dumpWriter->writeDump();
178 <    eorWriter->writeDump();
179 <
200 >  void VelocityVerletIntegrator::finalize() {
201 >    dumpWriter->writeEor();
202 >  
203 >    if (simParams->getUseSolidThermInt()) {
204 >      restWriter->writeZAngFile();
205 >      delete restWriter;
206 >      restWriter = NULL;
207 >    }
208 >  
209      delete dumpWriter;
181 –    delete eorWriter;
210      delete statWriter;
211 <
211 >  
212      dumpWriter = NULL;
185 –    eorWriter = NULL;
213      statWriter = NULL;
214 <    
215 < }
214 >  
215 >  }
216  
217 < void VelocityVerletIntegrator::integrateStep() {
218 <
217 >  void VelocityVerletIntegrator::integrateStep() {
218 >  
219      moveA();
220      calcForce(needPotential, needStress);
221      moveB();
222 < }
222 >  }
223  
224  
225 < void VelocityVerletIntegrator::calcForce(bool needPotential,
226 <                                         bool needStress) {
225 >  void VelocityVerletIntegrator::calcForce(bool needPotential,
226 >                                           bool needStress) {
227      forceMan_->calcForces(needPotential, needStress);
228 < }
228 >  }
229  
230 < DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
231 <    return new DumpWriter(info_, info_->getDumpFileName());
232 < }
230 >  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
231 >    return new DumpWriter(info_);
232 >  }
233  
234 < DumpWriter* VelocityVerletIntegrator::createEorWriter() {
208 <    return new DumpWriter(info_, getPrefix(info_->getDumpFileName()) + ".eor");
209 < }
234 >  StatWriter* VelocityVerletIntegrator::createStatWriter() {
235  
236 < StatWriter* VelocityVerletIntegrator::createStatWriter() {
237 <    return new StatWriter(info_->getStatFileName());
238 < }
236 >    std::string statFileFormatString = simParams->getStatFileFormat();
237 >    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
238 >    
239 >    // if solidThermInt is true, add extra information to the statfile
240 >    if (simParams->getUseSolidThermInt()){
241 >      mask.set(Stats::VRAW);
242 >      mask.set(Stats::VHARM);
243 >    }
244  
245 +    if (simParams->havePrintPressureTensor() &&
246 +        simParams->getPrintPressureTensor()){
247 +      mask.set(Stats::PRESSURE_TENSOR_XX);
248 +      mask.set(Stats::PRESSURE_TENSOR_XY);
249 +      mask.set(Stats::PRESSURE_TENSOR_XZ);
250 +      mask.set(Stats::PRESSURE_TENSOR_YX);
251 +      mask.set(Stats::PRESSURE_TENSOR_YY);
252 +      mask.set(Stats::PRESSURE_TENSOR_YZ);
253 +      mask.set(Stats::PRESSURE_TENSOR_ZX);
254 +      mask.set(Stats::PRESSURE_TENSOR_ZY);
255 +      mask.set(Stats::PRESSURE_TENSOR_ZZ);
256 +    }
257 +    
258 +    if (simParams->getAccumulateBoxDipole()) {
259 +      mask.set(Stats::BOX_DIPOLE_X);
260 +      mask.set(Stats::BOX_DIPOLE_Y);
261 +      mask.set(Stats::BOX_DIPOLE_Z);
262 +    }
263 +  
264 +    if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
265 +      if (simParams->getPrintTaggedPairDistance()) {
266 +        mask.set(Stats::TAGGED_PAIR_DISTANCE);
267 +      }
268 +    }
269  
270 +    if (simParams->getUseRNEMD()) {
271 +      mask.set(Stats::RNEMD_SWAP_TOTAL);
272 +    }
273 +      
274 +
275 +     return new StatWriter(info_->getStatFileName(), mask);
276 +  }
277 +
278 +  RestWriter* VelocityVerletIntegrator::createRestWriter(){
279 +    return new RestWriter(info_);
280 +  }
281 +
282 +
283   } //end namespace oopse

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