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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1126 by gezelter, Fri Apr 6 21:53:43 2007 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 94 | Line 94 | namespace oopse {
94  
95      dumpWriter->writeDumpAndEor();
96  
97 –    if (simParams->getUseSolidThermInt()) {
98 –      restWriter = createRestWriter();
99 –      restWriter->writeZAngFile();
100 –    }
101 –    
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 138 | 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 158 | Line 159 | namespace oopse {
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 <
165 <      if (simParams->getUseSolidThermInt())
166 <        restWriter->writeZAngFile();
167 <    
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 <      }
186 <  
191 >    
192 >    if (needReset && currentSnapshot_->getTime() >= currReset) {    
193 >      resetIntegrator();
194 >      currReset += resetTime;
195 >    }        
196    }
197  
198  
199    void VelocityVerletIntegrator::finalize() {
200      dumpWriter->writeEor();
201    
193 –    if (simParams->getUseSolidThermInt()) {
194 –      restWriter->writeZAngFile();
195 –      delete restWriter;
196 –      restWriter = NULL;
197 –    }
198 –  
202      delete dumpWriter;
203      delete statWriter;
204    
# Line 225 | 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() &&
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);
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()) {
# Line 250 | Line 260 | namespace oopse {
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 <     return new StatWriter(info_->getStatFileName(), mask);
271 <  }
270 >    if (simParams->getUseRNEMD()) {
271 >      mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272 >    }
273 >    
274  
275 <  RestWriter* VelocityVerletIntegrator::createRestWriter(){
258 <    return new RestWriter(info_);
275 >    return new StatWriter(info_->getStatFileName(), mask);
276    }
277  
278  
279 < } //end namespace oopse
279 > } //end namespace OpenMD

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