ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/integrators/VelocityVerletIntegrator.cpp
(Generate patch)

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/integrators/VelocityVerletIntegrator.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

# Line 36 | Line 36
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).                        
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 OpenMD {
57 <  VelocityVerletIntegrator::VelocityVerletIntegrator(SimInfo *info) : Integrator(info), rotAlgo(NULL) {
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 94 | Line 95 | namespace OpenMD {
95  
96      dumpWriter->writeDumpAndEor();
97  
98 +    progressBar = new ProgressBar();
99 +
100      //save statistics, before writeStat,  we must save statistics
101      thermo.saveStat();
102      saveConservedQuantity();
# Line 115 | Line 118 | namespace OpenMD {
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  
# Line 160 | Line 156 | namespace OpenMD {
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 OpenMD {
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 OpenMD {
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 OpenMD {
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()) {

Comparing:
trunk/src/integrators/VelocityVerletIntegrator.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 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
1 + Author Id Revision Date

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines