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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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();;
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      
# Line 137 | Line 139 | namespace oopse {
139    void VelocityVerletIntegrator::preStep() {
140      RealType difference = currentSnapshot_->getTime() + dt - currStatus;
141    
142 <    if (difference > 0 || fabs(difference) < oopse::epsilon) {
142 >    if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
143        needPotential = true;
144        needStress = true;  
145      }
# Line 150 | Line 152 | namespace oopse {
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 >      rnemd_->collectData();
164 >      if (currentSnapshot_->getTime() >= currRNEMD) {
165 >        rnemd_->doRNEMD();
166 >        currRNEMD += RNEMD_exchangeTime;
167 >      }
168 >    }
169 >    
170      if (currentSnapshot_->getTime() >= currSample) {
171        dumpWriter->writeDumpAndEor();
172 <    
164 <      if (simParams->getUseSolidThermInt())
165 <        restWriter->writeZangle();
166 <    
172 >      
173        currSample += sampleTime;
174      }
175 <  
175 >    
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 <    
186 >      
187        needPotential = false;
188        needStress = false;
189        currStatus += statusTime;
190      }
191 <
192 <      if (needReset && currentSnapshot_->getTime() >= currReset) {    
193 <        resetIntegrator();
194 <        currReset += resetTime;
195 <      }
185 <  
191 >    
192 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
193 >      resetIntegrator();
194 >      currReset += resetTime;
195 >    }        
196    }
197  
198  
199    void VelocityVerletIntegrator::finalize() {
200      dumpWriter->writeEor();
201    
192 –    if (simParams->getUseSolidThermInt()) {
193 –      restWriter->writeZangle();
194 –      delete restWriter;
195 –      restWriter = NULL;
196 –    }
197 –  
202      delete dumpWriter;
203      delete statWriter;
204    
# Line 224 | Line 228 | namespace oopse {
228  
229      std::string statFileFormatString = simParams->getStatFileFormat();
230      StatsBitSet mask = parseStatFileFormat(statFileFormatString);
231 <    
232 <    // if solidThermInt is true, add extra information to the statfile
233 <    if (simParams->getUseSolidThermInt()){
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() && simParams->getPrintPressureTensor()){
246 <        mask.set(Stats::PRESSURE_TENSOR_X);
247 <        mask.set(Stats::PRESSURE_TENSOR_Y);
248 <        mask.set(Stats::PRESSURE_TENSOR_Z);
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 <     return new StatWriter(info_->getStatFileName(), mask);
259 <  }
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 <  RestWriter* VelocityVerletIntegrator::createRestWriter(){
271 <    return new RestWriter(info_);
270 >    if (simParams->getUseRNEMD()) {
271 >      mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272 >    }
273 >    
274 >
275 >    return new StatWriter(info_->getStatFileName(), mask);
276    }
277  
278  
279 < } //end namespace oopse
279 > } //end namespace OpenMD

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