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Comparing trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents):
Revision 1341 by skuang, Fri May 8 19:47:05 2009 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_->getStatus();
101 >      rnemd_->getStarted();
102  
103      statWriter->writeStat(currentSnapshot_->statData);
104      
# Line 114 | Line 109 | namespace oopse {
109        currReset = resetTime + currentSnapshot_->getTime();
110      }
111      if (simParams->getUseRNEMD()){
112 <      currRNEMD = RNEMD_swapTime + currentSnapshot_->getTime();
112 >      currRNEMD = RNEMD_exchangeTime + currentSnapshot_->getTime();
113      }
114      needPotential = false;
115      needStress = false;      
# Line 144 | 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 165 | Line 160 | namespace oopse {
160        }
161      }
162      if (useRNEMD) {
163 +      rnemd_->collectData();
164        if (currentSnapshot_->getTime() >= currRNEMD) {
165 <        rnemd_->doSwap();
166 <        currRNEMD += RNEMD_swapTime;
165 >        rnemd_->doRNEMD();
166 >        currRNEMD += RNEMD_exchangeTime;
167        }
168      }
169      
170      if (currentSnapshot_->getTime() >= currSample) {
171        dumpWriter->writeDumpAndEor();
172        
177 –      if (simParams->getUseSolidThermInt())
178 –        restWriter->writeZAngFile();
179 –      
173        currSample += sampleTime;
174      }
175      
# Line 185 | Line 178 | namespace oopse {
178        thermo.saveStat();
179        saveConservedQuantity();
180  
181 <      if (simParams->getUseRNEMD())
181 >      if (simParams->getUseRNEMD()) {
182          rnemd_->getStatus();
183 +      }
184  
185        statWriter->writeStat(currentSnapshot_->statData);
186        
# Line 205 | Line 199 | namespace oopse {
199    void VelocityVerletIntegrator::finalize() {
200      dumpWriter->writeEor();
201    
208 –    if (simParams->getUseSolidThermInt()) {
209 –      restWriter->writeZAngFile();
210 –      delete restWriter;
211 –      restWriter = NULL;
212 –    }
213 –  
202      delete dumpWriter;
203      delete statWriter;
204    
# Line 240 | 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  
# Line 273 | Line 268 | namespace oopse {
268      }
269  
270      if (simParams->getUseRNEMD()) {
271 <      mask.set(Stats::RNEMD_SWAP_TOTAL);
271 >      mask.set(Stats::RNEMD_EXCHANGE_TOTAL);
272      }
273 <      
273 >    
274  
275 <     return new StatWriter(info_->getStatFileName(), mask);
275 >    return new StatWriter(info_->getStatFileName(), mask);
276    }
277  
283 –  RestWriter* VelocityVerletIntegrator::createRestWriter(){
284 –    return new RestWriter(info_);
285 –  }
278  
279 <
288 < } //end namespace oopse
279 > } //end namespace OpenMD

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