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Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1368 by skuang, Mon Oct 19 13:39:04 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 + * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
# Line 50 | Line 51
51   #include "integrators/VelocityVerletIntegrator.hpp"
52   #include "integrators/DLM.hpp"
53   #include "utils/StringUtils.hpp"
54 + #include "utils/ProgressBar.hpp"
55  
56 < namespace oopse {
57 <  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
56 > namespace OpenMD {
57 >  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info) {
58      dt2 = 0.5 * dt;
57 –    rotAlgo = new DLM();
58 –    rattle = new Rattle(info);
59    }
60    
61    VelocityVerletIntegrator::~VelocityVerletIntegrator() {
62 –    delete rotAlgo;
63 –    delete rattle;
62    }
63    
64    void VelocityVerletIntegrator::initialize(){
65      
66 <    forceMan_->init();
66 >    forceMan_->initialize();
67      
68      // remove center of mass drift velocity (in case we passed in a
69      // configuration that was drifting)
70      velocitizer_->removeComDrift();
71 +
72 +    // find the initial fluctuating charges.
73 +    flucQ_->initialize();
74      
75      // initialize the forces before the first step
76 <    calcForce(true, true);
76 >    calcForce();
77      
78      // execute the constraint algorithm to make sure that the system is
79      // constrained at the very beginning  
80      if (info_->getNGlobalConstraints() > 0) {
81 <      rattle->constraintA();
82 <      calcForce(true, true);
83 <      rattle->constraintB();      
81 >      rattle_->constraintA();
82 >      calcForce();
83 >      rattle_->constraintB();      
84        //copy the current snapshot to previous snapshot
85        info_->getSnapshotManager()->advance();
86      }
# Line 93 | Line 94 | namespace oopse {
94      statWriter = createStatWriter();
95  
96      dumpWriter->writeDumpAndEor();
97 +
98 +    progressBar = new ProgressBar();
99  
100      //save statistics, before writeStat,  we must save statistics
101      thermo.saveStat();
# Line 115 | Line 118 | namespace oopse {
118      needStress = false;      
119      
120    }
121 <
121 >
122    void VelocityVerletIntegrator::doIntegrate() {
123    
121 –  
124      initialize();
125    
126 <    while (currentSnapshot_->getTime() < runTime) {
127 <    
128 <      preStep();
129 <    
130 <      integrateStep();
129 <    
130 <      postStep();
131 <    
132 <    }
133 <  
126 >    while (currentSnapshot_->getTime() < runTime) {    
127 >      preStep();    
128 >      integrateStep();    
129 >      postStep();      
130 >    }  
131      finalize();
135 –  
132    }
133  
134  
135    void VelocityVerletIntegrator::preStep() {
136      RealType difference = currentSnapshot_->getTime() + dt - currStatus;
137    
138 <    if (difference > 0 || fabs(difference) < oopse::epsilon) {
138 >    if (difference > 0 || fabs(difference) < OpenMD::epsilon) {
139        needPotential = true;
140        needStress = true;  
141      }
# Line 160 | Line 156 | namespace oopse {
156        }
157      }
158      if (useRNEMD) {
163 –      rnemd_->collectData();
159        if (currentSnapshot_->getTime() >= currRNEMD) {
160          rnemd_->doRNEMD();
161          currRNEMD += RNEMD_exchangeTime;
162        }
163 +      rnemd_->collectData();
164      }
165      
166      if (currentSnapshot_->getTime() >= currSample) {
# Line 183 | Line 179 | namespace oopse {
179        }
180  
181        statWriter->writeStat(currentSnapshot_->statData);
182 <      
182 >
183 >      progressBar->setStatus(currentSnapshot_->getTime(), runTime);
184 >      progressBar->update();
185 >
186        needPotential = false;
187        needStress = false;
188        currStatus += statusTime;
# Line 204 | Line 203 | namespace oopse {
203    
204      dumpWriter = NULL;
205      statWriter = NULL;
207 –  
206    }
207  
208    void VelocityVerletIntegrator::integrateStep() {
209    
210      moveA();
211 <    calcForce(needPotential, needStress);
211 >    calcForce();
212      moveB();
213    }
214  
215  
216 <  void VelocityVerletIntegrator::calcForce(bool needPotential,
217 <                                           bool needStress) {
218 <    forceMan_->calcForces(needPotential, needStress);
216 >  void VelocityVerletIntegrator::calcForce() {
217 >    forceMan_->calcForces();
218 >    flucQ_->applyConstraints();
219    }
220  
221    DumpWriter* VelocityVerletIntegrator::createDumpWriter() {
# Line 260 | Line 258 | namespace oopse {
258        mask.set(Stats::BOX_DIPOLE_Y);
259        mask.set(Stats::BOX_DIPOLE_Z);
260      }
261 +
262 +    if (simParams->getPrintHeatFlux()) {
263 +      mask.set(Stats::HEATFLUX_X);
264 +      mask.set(Stats::HEATFLUX_Y);
265 +      mask.set(Stats::HEATFLUX_Z);
266 +    }
267    
268      if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) {
269        if (simParams->getPrintTaggedPairDistance()) {
# Line 276 | Line 280 | namespace oopse {
280    }
281  
282  
283 < } //end namespace oopse
283 > } //end namespace OpenMD

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1368 by skuang, Mon Oct 19 13:39:04 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

# Line 0 | Line 1
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