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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 1390 by gezelter, Wed Nov 25 20:02:06 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 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# Line 51 | Line 51
51   #include "integrators/DLM.hpp"
52   #include "utils/StringUtils.hpp"
53  
54 < namespace oopse {
54 > namespace OpenMD {
55    VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56      dt2 = 0.5 * dt;
57      rotAlgo = new DLM();
# 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_->getStarted();
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_exchangeTime + 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) < OpenMD::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 >      rnemd_->collectData();
164 >      if (currentSnapshot_->getTime() >= currRNEMD) {
165 >        rnemd_->doRNEMD();
166 >        currRNEMD += RNEMD_exchangeTime;
167 >      }
168 >    }
169      
170 <    if (simParams->getUseSolidThermInt())
171 <      restWriter->writeZangle();
170 >    if (currentSnapshot_->getTime() >= currSample) {
171 >      dumpWriter->writeDumpAndEor();
172 >      
173 >      currSample += sampleTime;
174 >    }
175      
176 <    currSample += sampleTime;
177 <  }
178 <  
179 <  if (currentSnapshot_->getTime() >= currStatus) {
180 <    //save statistics, before writeStat,  we must save statistics
181 <    thermo.saveStat();
182 <    saveConservedQuantity();
183 <    statWriter->writeStat(currentSnapshot_->statData);
184 <    
185 <    needPotential = false;
186 <    needStress = false;
187 <    currStatus += statusTime;
176 >    if (currentSnapshot_->getTime() >= currStatus) {
177 >      //save statistics, before writeStat,  we must save statistics
178 >      thermo.saveStat();
179 >      saveConservedQuantity();
180 >
181 >      if (simParams->getUseRNEMD()) {
182 >        rnemd_->getStatus();
183 >      }
184 >
185 >      statWriter->writeStat(currentSnapshot_->statData);
186 >      
187 >      needPotential = false;
188 >      needStress = false;
189 >      currStatus += statusTime;
190 >    }
191 >    
192 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
193 >      resetIntegrator();
194 >      currReset += resetTime;
195 >    }        
196    }
178 –  
179 –  
180 – }
197  
198  
199 < void VelocityVerletIntegrator::finalize() {
200 <  dumpWriter->writeEor();
199 >  void VelocityVerletIntegrator::finalize() {
200 >    dumpWriter->writeEor();
201    
202 <  if (simParams->getUseSolidThermInt()) {
203 <    restWriter->writeZangle();
188 <    delete restWriter;
189 <    restWriter = NULL;
190 <  }
202 >    delete dumpWriter;
203 >    delete statWriter;
204    
205 <  delete dumpWriter;
206 <  delete statWriter;
205 >    dumpWriter = NULL;
206 >    statWriter = NULL;
207    
208 <  dumpWriter = NULL;
196 <  statWriter = NULL;
197 <  
198 < }
208 >  }
209  
210 < void VelocityVerletIntegrator::integrateStep() {
210 >  void VelocityVerletIntegrator::integrateStep() {
211    
212 <  moveA();
213 <  calcForce(needPotential, needStress);
214 <  moveB();
215 < }
212 >    moveA();
213 >    calcForce(needPotential, needStress);
214 >    moveB();
215 >  }
216  
217  
218 < void VelocityVerletIntegrator::calcForce(bool needPotential,
219 <                                         bool needStress) {
220 <  forceMan_->calcForces(needPotential, needStress);
221 < }
218 >  void VelocityVerletIntegrator::calcForce(bool needPotential,
219 >                                           bool needStress) {
220 >    forceMan_->calcForces(needPotential, needStress);
221 >  }
222  
223 < DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224 <  return new DumpWriter(info_);
225 < }
223 >  DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
224 >    return new DumpWriter(info_);
225 >  }
226  
227 < StatWriter* VelocityVerletIntegrator::createStatWriter() {
228 <  // if solidThermInt is true, add extra information to the statfile
229 <  if (simParams->getUseSolidThermInt()){
230 <    StatsBitSet mask;
231 <    mask.set(Stats::TIME);
232 <    mask.set(Stats::TOTAL_ENERGY);
233 <    mask.set(Stats::POTENTIAL_ENERGY);
234 <    mask.set(Stats::KINETIC_ENERGY);
235 <    mask.set(Stats::TEMPERATURE);
236 <    mask.set(Stats::PRESSURE);
237 <    mask.set(Stats::CONSERVED_QUANTITY);
238 <    mask.set(Stats::VRAW);
239 <    mask.set(Stats::VHARM);
227 >  StatWriter* VelocityVerletIntegrator::createStatWriter() {
228 >
229 >    std::string statFileFormatString = simParams->getStatFileFormat();
230 >    StatsBitSet mask = parseStatFileFormat(statFileFormatString);
231 >  
232 >    // if we're doing a thermodynamic integration, we'll want the raw
233 >    // potential as well as the full potential:
234 >
235 >
236 >    if (simParams->getUseThermodynamicIntegration())
237 >      mask.set(Stats::VRAW);
238 >
239 >    // if we've got restraints turned on, we'll also want a report of the
240 >    // total harmonic restraints
241 >    if (simParams->getUseRestraints()){
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_EXCHANGE_TOTAL);
272 >    }
273 >    
274 >
275      return new StatWriter(info_->getStatFileName(), mask);
276    }
232 –  
233 –  return new StatWriter(info_->getStatFileName());
234 – }
277  
236 – RestWriter* VelocityVerletIntegrator::createRestWriter(){
237 –  return new RestWriter(info_);
238 – }
278  
279 <
241 < } //end namespace oopse
279 > } //end namespace OpenMD

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